Pub Date : 2026-01-05DOI: 10.1016/j.jgeb.2025.100654
K.M. Tanjida Islam, Roksana Khanam, Shahin Mahmud
With cancer causing over 10 million deaths annually, identifying novel therapeutic targets is crucial. SIRT7 is a NAD-dependent deacetylase that regulates oncogenic pathways, making it a promising therapeutic target. However, no approved medications currently exist against SIRT7, and available inhibitors exhibit limited efficacy alongside significant toxicity. Therefore, this study explores marine biodiversity as a source of SIRT7 inhibitors. Molecular docking screening of SIRT7 identified four promising marine phytochemicals (CMNPD28383, CMNPD24305, CMNPD24304, CMNPD14924) with superior binding affinities (−9.9 to −8.4 kcal/mol). Molecular dynamics simulations confirmed stable protein–ligand complexes with RMSD variations of 4.714 to 6.905 Å. Most of these phytochemicals demonstrated favorable ADMET profiles, high oral bioavailability, strong predicted anticancer activity (Pa > 0,6), and potent machine learning (RandomForest Cross Validation R2 = 0.8614 ± 0.0244) predicted inhibitory activity (pIC50: −2.110 to −2.875; IC50: 129 nM to 749 nM). Therefore, these marine phytochemicals could be potential novel SIRT7 inhibitors with excellent drug-like properties, providing a foundation for further experimental validation and potential clinical translation. In addition, these computational approaches offer a promising avenue to develop safer and effective cancer therapeutics from marine sources.
{"title":"Computational discovery of marine natural phytochemicals as novel SIRT7 inhibitors for cancer treatment","authors":"K.M. Tanjida Islam, Roksana Khanam, Shahin Mahmud","doi":"10.1016/j.jgeb.2025.100654","DOIUrl":"10.1016/j.jgeb.2025.100654","url":null,"abstract":"<div><div>With cancer causing over 10 million deaths annually, identifying novel therapeutic targets is crucial. SIRT7 is a NAD-dependent deacetylase that regulates oncogenic pathways, making it a promising therapeutic target. However, no approved medications currently exist against SIRT7, and available inhibitors exhibit limited efficacy alongside significant toxicity. Therefore, this study explores marine biodiversity as a source of SIRT7 inhibitors. Molecular docking screening of SIRT7 identified four promising marine phytochemicals (CMNPD28383, CMNPD24305, CMNPD24304, CMNPD14924) with superior binding affinities (−9.9 to −8.4 kcal/mol). Molecular dynamics simulations confirmed stable protein–ligand complexes with RMSD variations of 4.714 to 6.905 Å. Most of these phytochemicals demonstrated favorable ADMET profiles, high oral bioavailability, strong predicted anticancer activity (Pa > 0,6), and potent machine learning (RandomForest Cross Validation R<sup>2</sup> = 0.8614 ± 0.0244) predicted inhibitory activity (pIC<sub>50</sub>: −2.110 to −2.875; IC<sub>50</sub>: 129 nM to 749 nM). Therefore, these marine phytochemicals could be potential novel SIRT7 inhibitors with excellent drug-like properties, providing a foundation for further experimental validation and potential clinical translation. In addition, these computational approaches offer a promising avenue to develop safer and effective cancer therapeutics from marine sources.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100654"},"PeriodicalIF":2.8,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145939431","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 : 2026-01-05DOI: 10.1016/j.jgeb.2025.100639
Moshira Ghaleb, Maryam Al-Berry, Hala Ebied, Mohamed Tolba
Cancer remains a critical global health challenge, driving the need for innovative approaches in diagnosis and treatment. This research introduces OmicsFusionNet, an AI-powered hybrid model integrating machine learning and deep learning to revolutionize cancer care. The tool incorporates up to six multiomics datasets—genomics, transcriptomics, and epigenomics—achieving 80.2% accuracy across 23 cancer types. Notably, RNAseq and methylation integration reached 99.8% accuracy, highlighting XGBoost’s feature selection and deep learning’s classification strength.
For ovarian cancer stage detection, OmicsFusionNet optimized analysis using CPTAC-OV and TCGA-OV datasets, achieving accuracies between 83% and 91% by combining ElasticNet and XGBoost with deep learning. Additionally, KEGG pathway enrichment of multiomics biomarkers identified key cancer-related pathways, advancing early detection, biomarker discovery, and personalized treatments.
This study underscores the transformative potential of AI and multiomics integration in cancer research, enabling precise interventions and uncovering novel mechanisms that enhance patient outcomes.
{"title":"AI based multiomics integration for cancer diagnosis and prognosis","authors":"Moshira Ghaleb, Maryam Al-Berry, Hala Ebied, Mohamed Tolba","doi":"10.1016/j.jgeb.2025.100639","DOIUrl":"10.1016/j.jgeb.2025.100639","url":null,"abstract":"<div><div>Cancer remains a critical global health challenge, driving the need for innovative approaches in diagnosis and treatment. This research introduces OmicsFusionNet, an AI-powered hybrid model integrating machine learning and deep learning to revolutionize cancer care. The tool incorporates up to six multiomics datasets—genomics, transcriptomics, and epigenomics—achieving 80.2% accuracy across 23 cancer types. Notably, RNAseq and methylation integration reached 99.8% accuracy, highlighting XGBoost’s feature selection and deep learning’s classification strength.</div><div>For ovarian cancer stage detection, OmicsFusionNet optimized analysis using CPTAC-OV and TCGA-OV datasets, achieving accuracies between 83% and 91% by combining ElasticNet and XGBoost with deep learning. Additionally, KEGG pathway enrichment of multiomics biomarkers identified key cancer-related pathways, advancing early detection, biomarker discovery, and personalized treatments.</div><div>This study underscores the transformative potential of AI and multiomics integration in cancer research, enabling precise interventions and uncovering novel mechanisms that enhance patient outcomes.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100639"},"PeriodicalIF":2.8,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145939429","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}
Tomato brown rugose fruit virus (ToBRFV), a highly virulent tobamovirus, poses a major threat to global tomato production by overcoming host resistance and traditional control measures. This study evaluates the efficacy of low-dose gamma irradiation (10, 15, and 20 Gy) in reducing ToBRFV contamination in tomato seeds. Contaminated seeds were irradiated and assessed for germination rate, chlorophyll content, stem diameter, and viral accumulation with RT-qPCR. The potential synergistic effect of combining 15 Gy gamma irradiation with 2.5 % sodium hypochlorite (NaOCl) was also investigated. Results revealed that 15 Gy significantly improved germination, enhanced chlorophyll levels, and increased stem thickness, while substantially reducing viral replication. In contrast, 20 Gy had detrimental effects on both plant growth and viral suppression. The combination of 15 Gy and NaOCl further decreased viral accumulation, though at the cost of reduced germination rates. Applying 15 Gy confers dual benefits, including effective seed disinfection and improved host resistance. It shows strong potential for use in integrated tomato disease management in greenhouse and field conditions.
{"title":"Effect of low-dose gamma irradiation on seed-borne transmission of tomato brown rugose fruit virus in tomato","authors":"Kimia Tokhmechi , Abozar Ghorbani , Davoud Koolivand , Mahsa Rostami , Nahid Hajiloo","doi":"10.1016/j.jgeb.2025.100644","DOIUrl":"10.1016/j.jgeb.2025.100644","url":null,"abstract":"<div><div>Tomato brown rugose fruit virus (ToBRFV), a highly virulent tobamovirus, poses a major threat to global tomato production by overcoming host resistance and traditional control measures. This study evaluates the efficacy of low-dose gamma irradiation (10, 15, and 20 Gy) in reducing ToBRFV contamination in tomato seeds. Contaminated seeds were irradiated and assessed for germination rate, chlorophyll content, stem diameter, and viral accumulation with RT-qPCR. The potential synergistic effect of combining 15 Gy gamma irradiation with 2.5 % sodium hypochlorite (NaOCl) was also investigated. Results revealed that 15 Gy significantly improved germination, enhanced chlorophyll levels, and increased stem thickness, while substantially reducing viral replication. In contrast, 20 Gy had detrimental effects on both plant growth and viral suppression. The combination of 15 Gy and NaOCl further decreased viral accumulation, though at the cost of reduced germination rates. Applying 15 Gy confers dual benefits, including effective seed disinfection and improved host resistance. It shows strong potential for use in integrated tomato disease management in greenhouse and field conditions.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100644"},"PeriodicalIF":2.8,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145939432","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 : 2026-01-03DOI: 10.1016/j.jgeb.2025.100643
Shahzadi Asia Nadeem , Ijaz Ali , Hazrat Hussain , Ihsan Ullah , Wajid Ali , Khalid J. Alzahrani , Hamid Ali , Zarak Imtiaz Khan , Kasim Sakran Abass , Rafi ur Rahman
Background
The complicated relationship between the Aedes mosquito microbiome, arbovirus transmission and essential physiological processes, is extremely important. Microbial community plays a vital role in shaping vector biology, impacting critical aspects such as parasite replication within the vector, vector longevity, and ultimately, vector competence. Understanding the composition and function of the Aedes microbiome is therefore crucial for developing novel strategies to control arboviral diseases. Therefore, we aimed to identify prevalent bacterial and viral communities in Aedes mosquitoes from Pakistan.
Methods
Ae. aegypti and Ae. albopictus were collected and from three different regions of Khyber Pakhtoonkhwa, Punjab and federal capital Islamabad. We isolated DNA and sequenced two pools of each species and conducted metagenomic analysis, identifying a variety of bacteria and viruses.
Results
We found diverse bacterial and viral communities in both studied species. In Ae. aegypti, the most abundant bacterial species was Klebsiella pneumoniae followed by Acinetobacter baylyi. Ae. albopictus presented Pseudomonas putida as the most abundant bacterial species followed by Brevundimonas diminuta. Similarly in Ae. aegypti, we found that Escherichia phage HK639 was the most abundant viral species while in Ae. albopictus, it was Lactobacillus phage 2. It is important to mention that the prevalent viruses in both Aedes species belong to the Siphoviridae genus.
{"title":"Metagenomic analysis of bacterial and viral communities of Aedes aegypti and Aedes albopictus","authors":"Shahzadi Asia Nadeem , Ijaz Ali , Hazrat Hussain , Ihsan Ullah , Wajid Ali , Khalid J. Alzahrani , Hamid Ali , Zarak Imtiaz Khan , Kasim Sakran Abass , Rafi ur Rahman","doi":"10.1016/j.jgeb.2025.100643","DOIUrl":"10.1016/j.jgeb.2025.100643","url":null,"abstract":"<div><h3>Background</h3><div>The complicated relationship between the <em>Aedes</em> mosquito microbiome, arbovirus transmission and essential physiological processes, is extremely important. Microbial community plays a vital role in shaping vector biology, impacting critical aspects such as parasite replication within the vector, vector longevity, and ultimately, vector competence. Understanding the composition and function of the <em>Aedes</em> microbiome is therefore crucial for developing novel strategies to control arboviral diseases. Therefore, we aimed to identify prevalent bacterial and viral communities in <em>Aedes</em> mosquitoes from Pakistan.</div></div><div><h3>Methods</h3><div><em>Ae. aegypti</em> and <em>Ae. albopictus</em> were collected and from three different regions of Khyber Pakhtoonkhwa, Punjab and federal capital Islamabad. We isolated DNA and sequenced two pools of each species and conducted metagenomic analysis, identifying a variety of bacteria and viruses.</div></div><div><h3>Results</h3><div>We found diverse bacterial and viral communities in both studied species. In <em>Ae. aegypti</em>, the most abundant bacterial species was <em>Klebsiella pneumoniae</em> followed by <em>Acinetobacter baylyi</em>. <em>Ae. albopictus</em> presented <em>Pseudomonas putida</em> as the most abundant bacterial species followed by <em>Brevundimonas diminuta</em>. Similarly in <em>Ae. aegypti</em>, we found that <em>Escherichia phage</em> HK639 was the most abundant viral species while in <em>Ae. albopictus</em>, it was <em>Lactobacillus phage</em> 2. It is important to mention that the prevalent viruses in both <em>Aedes</em> species belong to the <em>Siphoviridae</em> genus.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100643"},"PeriodicalIF":2.8,"publicationDate":"2026-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145939430","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 : 2026-01-02DOI: 10.1016/j.jgeb.2025.100646
Mohamed Khedr , Ahmed E.M. Abdelaziz , Fatima Albadwi , Fady Sayed Youssef , Eman M. Abd El-maksoud , Alsayed E. Mekky , Ebrahim Saied , Mohamed A.M. El-Tabakh , Eslam S Abdelmouty , Jayda G. Eldiasty , Mohammad Y. Alfaifih , Ali A. Shatii , Serag Eldin I. Elbehairii , Mohammed Aufy
Astragalus membranaceus is a traditional medicinal plant with diverse therapeutic properties largely attributed to its polysaccharides (APs). This study evaluated the antimicrobial, anti-inflammatory, antioxidant, and anticancer activities of APs and eugenol, both individually and in combination, against multidrug-resistant (MDR) pathogens and HepG2 liver cancer cells. Thirty bacterial and ten Candida isolates were recovered from skin abscesses, with five identified as MDR strains (Staphylococcus haemolyticus, S. aureus, E. coli, Acinetobacter baumannii, and Candida auris), confirmed by 16S rDNA and ITS sequencing. Both APs and eugenol exhibited marked antimicrobial activity, while their combination achieved the strongest inhibition (up to 27.3 ± 0.4 mm). C. auris was highly sensitive to APs alone (MIC: 2 ± 0.2 µg/mL). The combination also significantly downregulated IL-6, IL-17, and TNF-α levels, and showed potent COX-2 inhibition (0.10 ± 0.01 µg/mL), surpassing celecoxib (0.9 ± 0.05 µg/mL). Antioxidant analysis (DPPH assay) revealed superior radical scavenging by the combination (57.5 ± 1.3 % %). Molecular docking confirmed the activity of eugenol, showing favorable binding to DNA gyrase B, sterol demethylase, COX-2, xanthine oxidase, and caspase-3, with the strongest affinity for xanthine oxidase (−5.25 kcal/mol). In anticancer assays, eugenol induced dose-dependent inhibition of HepG2 cell proliferation, while APs displayed limited cytotoxicity. Notably, the combination reduced cell viability to 3.77 ± 0.4 % % at 400 µg/mL, consistent with apoptotic changes. Collectively, these findings highlight the synergistic potential of APs and eugenol as a multi-target therapeutic approach against MDR infections, inflammation, oxidative stress, and liver cancer.
{"title":"Astragalus membranaceus polysaccharide (APs) and Eugenol: Multi-target Anti-inflammatory, Antioxidant, Antimicrobial, and anticancer effects validated by in Silico studies","authors":"Mohamed Khedr , Ahmed E.M. Abdelaziz , Fatima Albadwi , Fady Sayed Youssef , Eman M. Abd El-maksoud , Alsayed E. Mekky , Ebrahim Saied , Mohamed A.M. El-Tabakh , Eslam S Abdelmouty , Jayda G. Eldiasty , Mohammad Y. Alfaifih , Ali A. Shatii , Serag Eldin I. Elbehairii , Mohammed Aufy","doi":"10.1016/j.jgeb.2025.100646","DOIUrl":"10.1016/j.jgeb.2025.100646","url":null,"abstract":"<div><div><em>Astragalus membranaceus</em> is a traditional medicinal plant with diverse therapeutic properties largely attributed to its polysaccharides (APs). This study evaluated the antimicrobial, anti-inflammatory, antioxidant, and anticancer activities of APs and eugenol, both individually and in combination, against multidrug-resistant (MDR) pathogens and HepG2 liver cancer cells. Thirty bacterial and ten <em>Candida</em> isolates were recovered from skin abscesses, with five identified as MDR strains (<em>Staphylococcus haemolyticus, S. aureus, E. coli, Acinetobacter baumannii</em>, and <em>Candida auris</em>), confirmed by 16S rDNA and ITS sequencing. Both APs and eugenol exhibited marked antimicrobial activity, while their combination achieved the strongest inhibition (up to 27.3 ± 0.4 mm). <em>C. auris</em> was highly sensitive to APs alone (MIC: 2 ± 0.2 µg/mL). The combination also significantly downregulated IL-6, IL-17, and TNF-α levels, and showed potent COX-2 inhibition (0.10 ± 0.01 µg/mL), surpassing celecoxib (0.9 ± 0.05 µg/mL). Antioxidant analysis (DPPH assay) revealed superior radical scavenging by the combination (57.5 ± 1.3 % %). Molecular docking confirmed the activity of eugenol, showing favorable binding to DNA gyrase B, sterol demethylase, COX-2, xanthine oxidase, and caspase-3, with the strongest affinity for xanthine oxidase (−5.25 kcal/mol). In anticancer assays, eugenol induced dose-dependent inhibition of HepG2 cell proliferation, while APs displayed limited cytotoxicity. Notably, the combination reduced cell viability to 3.77 ± 0.4 % % at 400 µg/mL, consistent with apoptotic changes. Collectively, these findings highlight the synergistic potential of APs and eugenol as a multi-target therapeutic approach against MDR infections, inflammation, oxidative stress, and liver cancer.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100646"},"PeriodicalIF":2.8,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145884540","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 : 2025-12-31DOI: 10.1016/j.jgeb.2025.100656
Fatina I. Fadel , Khalda Amr , Rasha EssamEldin Galal , Ghada El-kamah , Mohamed A Abdel Mawla , Amr Mohamed Salem , Mohamed S. Thabet , Shorouk A.Othman
Background
Atypical hemolytic uremic syndrome (aHUS) is a rare, severe condition in children, resulting from uncontrolled complement activation caused by genetic factors or autoantibodies; it usually has a poor prognosis. Early identification of the underlying genetic variants is crucial for guiding management and predicting outcomes. This study aimed to identify gene mutations in Egyptian children with aHUS at an early stage. This would enable the selection of the most appropriate treatment options and help prevent adverse outcomes for the patients.
Methods
This is an observational cohort study, included 21 children with a clinical diagnosis of aHUS who presented to the Pediatric Nephrology Unit and general wards of Cairo University Children’s Hospital between June 2022 and January 2024 with a follow-up duration of 12 months (median). All patients underwent whole exome sequencing (WES). Clinical data, treatment regimens, and outcomes were recorded and analyzed.
Result
Among the 21 patients, around one third had negative WES results while 28.57 % showed CFHR 3/CFHR1 deletion. Most patients progressed to chronic kidney disease (52.4 %), while 28.6 % recovered their kidney functions following plasmapheresis. A significant association was observed between WES category and disease relapse (p = 0.021); patients with CFHR3 deletion, CFHR5 deletion, or MMUT variant developed at least one attack of relapse.
Conclusions
Egyptian children with aHUS demonstrate marked genetic heterogeneity. A substantial proportion lacked identifiable pathogenic variants, highlighting the complexity of the disease. CFHR3/CFHR1 deletion was the most frequent finding. Genetic profiling remains crucial for anticipating relapse risk and guiding therapeutic decisions, particularly in resource-limited settings.
{"title":"Comprehensive gene profiling by Next-Generation sequencing in a cohort of Egyptian pediatric Atypical HUS","authors":"Fatina I. Fadel , Khalda Amr , Rasha EssamEldin Galal , Ghada El-kamah , Mohamed A Abdel Mawla , Amr Mohamed Salem , Mohamed S. Thabet , Shorouk A.Othman","doi":"10.1016/j.jgeb.2025.100656","DOIUrl":"10.1016/j.jgeb.2025.100656","url":null,"abstract":"<div><h3>Background</h3><div>Atypical hemolytic uremic syndrome (aHUS) is a rare, severe condition in children, resulting from uncontrolled complement activation caused by genetic factors or autoantibodies; it usually has a poor prognosis. Early identification of the underlying genetic variants is crucial for guiding management and predicting outcomes. This study aimed to identify gene mutations in Egyptian children with aHUS at an early stage. This would enable the selection of the most appropriate treatment options and help prevent adverse outcomes for the patients<strong>.</strong></div></div><div><h3>Methods</h3><div>This is an observational cohort study, included 21 children with a clinical diagnosis of aHUS who presented to the Pediatric Nephrology Unit and general wards of Cairo University Children’s Hospital between June 2022 and January 2024 with a follow-up duration of 12 months (median). All patients underwent whole exome sequencing (WES). Clinical data, treatment regimens, and outcomes were recorded and analyzed.</div></div><div><h3>Result</h3><div>Among the 21 patients, around one third had negative WES results while 28.57 % showed CFHR 3/CFHR1 deletion. Most patients progressed to chronic kidney disease (52.4 %), while 28.6 % recovered their kidney functions following plasmapheresis. A significant association was observed between WES category and disease relapse (p = 0.021); patients with CFHR3 deletion, CFHR5 deletion, or MMUT variant developed at least one attack of relapse.</div></div><div><h3>Conclusions</h3><div>Egyptian children with aHUS demonstrate marked genetic heterogeneity. A substantial proportion lacked identifiable pathogenic variants, highlighting the complexity of the disease. CFHR3/CFHR1 deletion was the most frequent finding. Genetic profiling remains crucial for anticipating relapse risk and guiding therapeutic decisions, particularly in resource-limited settings.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100656"},"PeriodicalIF":2.8,"publicationDate":"2025-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145884541","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 : 2025-12-28DOI: 10.1016/j.jgeb.2025.100645
Amani Kenaan Abd-Alrahman, Huda SA. AL-Hayanni
Multidrug-resistant Klebsiella pneumoniae poses a serious clinical threat because of its ability to form biofilms and generate extended-spectrum beta-lactamase enzymes (ESBLs). This research investigated the influence of biosynthesized zinc oxide nanoparticles made from Fusarium oxysporum alcohol extract (FOE) on ESBL genes (blaTEM, blaCTX-M, blaSHV) and the biofilm-associated genes mrkA and luxS. The presence of the 16S rRNA, ESBL and biofilm genes was confirmed through subsequent polymerase chain reaction of the isolates. The FOE and zinc oxide nanoparticles both demonstrated significant antibacterial activity, with zinc oxide nanoparticles exhibiting greater inhibition with a minimum inhibitory concentration (MIC) of 26 μg/ml. Compared with untreated and FOE-treated isolates, those treated with sub-MIC concentrations of zinc oxide nanoparticles expressed significantly fewer ESBL and biofilm-related genes. The expression levels of the genes blaTEM, blaCTX-M, blaSHV, mrkA and luxS were downregulated below a ratio of 1.0 in each of the bacterial isolates. The biosynthesized zinc oxide nanoparticles demonstrated strong antibacterial and antibiofilm effects through the downregulation of bacterial antibiotic resistance and virulence genes in K. pneumoniae. The findings of this study demonstrate the ability of biosynthesized zinc oxide nanoparticles to function as a green and apotential alternative or support the role of antibiotcs for the treatment of multidrug-resistant (MDR) bacteria.
{"title":"Bioactivity of green-synthesized zinc oxide nanoparticles using Fusarium oxysporum extract on the expression of extended-spectrum beta-lactamase and biofilm-associated genes in the pathogen Klebsiella pneumoniae","authors":"Amani Kenaan Abd-Alrahman, Huda SA. AL-Hayanni","doi":"10.1016/j.jgeb.2025.100645","DOIUrl":"10.1016/j.jgeb.2025.100645","url":null,"abstract":"<div><div>Multidrug-resistant <em>Klebsiella pneumoniae</em> poses a serious clinical threat because of its ability to form biofilms and generate extended-spectrum beta-lactamase enzymes (ESBLs). This research investigated the influence of biosynthesized zinc oxide nanoparticles made from <em>Fusarium oxysporum</em> alcohol extract (FOE) on ESBL genes (<em>bla</em>TEM, <em>bla</em>CTX-M, <em>bla</em>SHV) and the biofilm-associated genes <em>mrk</em>A and <em>lux</em>S. The presence of the 16S rRNA, ESBL and biofilm genes was confirmed through subsequent polymerase chain reaction of the isolates. The FOE and zinc oxide nanoparticles both demonstrated significant antibacterial activity, with zinc oxide nanoparticles exhibiting greater inhibition with a minimum inhibitory concentration (MIC) of 26 μg/ml. Compared with untreated and FOE-treated isolates, those treated with sub-MIC concentrations of zinc oxide nanoparticles expressed significantly fewer ESBL and biofilm-related genes. The expression levels of the genes <em>bla</em>TEM, <em>bla</em>CTX-M, <em>bla</em>SHV, <em>mrk</em>A and <em>lux</em>S were downregulated below a ratio of 1.0 in each of the bacterial isolates. The biosynthesized zinc oxide nanoparticles demonstrated strong antibacterial and antibiofilm effects through the downregulation of bacterial antibiotic resistance and virulence genes in <em>K. pneumoniae</em>. The findings of this study demonstrate the ability of biosynthesized zinc oxide nanoparticles to function as a green and apotential alternative or support the role of antibiotcs for the treatment of multidrug-resistant (MDR) bacteria.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100645"},"PeriodicalIF":2.8,"publicationDate":"2025-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145884542","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 : 2025-12-26DOI: 10.1016/j.jgeb.2025.100649
Shraboni Mostofa Shila, Asfi Raian Ome, Ashfaque Ahmed, Rupa Rani Roy, Mohammad Ashraful Alam
This study analyzed the genetic diversity and population structure of Mesua ferrea L. in Bangladesh using Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat (ISSR) markers. A total of 63 individuals from six geographically distinct populations were analyzed. Thirty-nine and eighty-five polymorphic bands were generated using RAPD and ISSR primers, respectively, both showing 100 % polymorphism. ISSR markers showed higher polymorphic information content (PIC) (0.336 ± 0.055) and resolving power (Rp) (3.550 ± 1.47) than RAPD (PIC: 0.320 ± 0.055; Rp: 1.582 ± 0.813), indicating greater efficiency in detecting genetic variation. Genetic diversity parameters revealed substantial variability, with the Moulvibazar and BFRI populations showing the highest Nei’s diversity and Shannon indices. UPGMA dendrograms and Principal Coordinate Analysis (PCoA) indicated two major genetic clusters with significant overlap among populations, reflecting weak genetic structuring and strong gene flow. STRUCTURE analysis identified four and three genetic clusters (K = 4 and K = 3) for RAPD and ISSR data, respectively, confirming admixture among populations. AMOVA revealed that 65–77 % of total genetic variation occurred within populations, while 6–17 % was among populations, signifying moderate differentiation. The findings demonstrate high within-population diversity and genetic connectivity across regions. ISSR markers exhibited superior resolution, whereas RAPD captured broader inter-population relationships. Overall, the combined use of RAPD and ISSR markers provided complementary insights into the genetic architecture of M. ferrea. Populations from Moulvibazar, BFRI, and SUST, identified as genetically diverse and admixed, are recommended as priority sources for conservation, restoration, and breeding programs to ensure long-term genetic sustainability of the species.
{"title":"Unraveling the genetic diversity and population structure of Mesua ferrea L. Through RAPD and ISSR markers for effective conservation","authors":"Shraboni Mostofa Shila, Asfi Raian Ome, Ashfaque Ahmed, Rupa Rani Roy, Mohammad Ashraful Alam","doi":"10.1016/j.jgeb.2025.100649","DOIUrl":"10.1016/j.jgeb.2025.100649","url":null,"abstract":"<div><div>This study analyzed the genetic diversity and population structure of <em>Mesua ferrea</em> L. in Bangladesh using Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat (ISSR) markers. A total of 63 individuals from six geographically distinct populations were analyzed. Thirty-nine and eighty-five polymorphic bands were generated using RAPD and ISSR primers, respectively, both showing 100 % polymorphism. ISSR markers showed higher polymorphic information content (PIC) (0.336 ± 0.055) and resolving power (Rp) (3.550 ± 1.47) than RAPD (PIC: 0.320 ± 0.055; Rp: 1.582 ± 0.813), indicating greater efficiency in detecting genetic variation. Genetic diversity parameters revealed substantial variability, with the Moulvibazar and BFRI populations showing the highest Nei’s diversity and Shannon indices. UPGMA dendrograms and Principal Coordinate Analysis (PCoA) indicated two major genetic clusters with significant overlap among populations, reflecting weak genetic structuring and strong gene flow. STRUCTURE analysis identified four and three genetic clusters (K = 4 and K = 3) for RAPD and ISSR data, respectively, confirming admixture among populations. AMOVA revealed that 65–77 % of total genetic variation occurred within populations, while 6–17 % was among populations, signifying moderate differentiation. The findings demonstrate high within-population diversity and genetic connectivity across regions. ISSR markers exhibited superior resolution, whereas RAPD captured broader inter-population relationships. Overall, the combined use of RAPD and ISSR markers provided complementary insights into the genetic architecture of <em>M. ferrea</em>. Populations from Moulvibazar, BFRI, and SUST, identified as genetically diverse and admixed, are recommended as priority sources for conservation, restoration, and breeding programs to ensure long-term genetic sustainability of the species.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100649"},"PeriodicalIF":2.8,"publicationDate":"2025-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145841422","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 : 2025-12-24DOI: 10.1016/j.jgeb.2025.100650
Hassan Abolghasemi , Hamidreza Kheiri , Hamid Sedighian , Elham Behzadi , Reza Kachuei , Mozhgan Kheirandish , Masoud Arabfard , Abbas Ali Imani Fooladi
Background
SARS-CoV-2 causes mortality in a considerable number of patients with COVID-19. The association of comorbidities and gender with the expression of lncRNAs and mRNAs in COVID-19 patients is not fully understood. The purpose of the present study was to explore this association.
Method
We used Transcriptomics data for lncRNAs and mRNAs from the integrated Gene Expression Omnibus (GEO) to identify Differentially Expressed Genes (DEGs) using R software for statistical and data analysis. Then, we carried out Gene Ontology (GO) analysis and constructed a Protein-Protein Interaction (PPI) network to identify interactions between the genes.
Results
In this study, we divided samples into four groups and compared Differentially Expressed lncRNAs (DEls) and DEGs. Genes enriched in immune response and cytokine pathways were identified by GO analysis. By considering the protein–protein interaction network, the hub genes were ALAS2, CCL2, AHSP, and IL5.
Conclusion
mRNAs and lncRNAs could be used to identify the effects of SARS-CoV-2 on defined parameters (such as gender, main comorbidities in recovery, and treatment stages). Heme/hemoglobin metabolism was enriched in groups 1, 2, and 4, with four common genes (ALAS2, AHSP, HBD, and CA1) that are associated with the immune response to infection. CCL2 was enriched in group 3 and its expression was remarkably high in patients with an unfavorable outcome compared to other cases. Also, while both IL-5 and ALAS2 were enriched in group 4, IL-5 appeared to have no significant role in COVID-19. Overall, we conducted a bioinformatics analysis to predict how mRNAs and lncRNAs interact in patients with different characteristics such as gender, underlying disease, and treatment or recovery stages. mRNAs and lncRNAs can be potential biomarkers to examine the effect of SARS-CoV-2 on defined parameters.
{"title":"Association of gender and main comorbidities with expression of lncRNAs and mRNAs in COVID-19 patients","authors":"Hassan Abolghasemi , Hamidreza Kheiri , Hamid Sedighian , Elham Behzadi , Reza Kachuei , Mozhgan Kheirandish , Masoud Arabfard , Abbas Ali Imani Fooladi","doi":"10.1016/j.jgeb.2025.100650","DOIUrl":"10.1016/j.jgeb.2025.100650","url":null,"abstract":"<div><h3>Background</h3><div>SARS-CoV-2 causes mortality in a considerable number of patients with COVID-19. The association of comorbidities and gender with the expression of lncRNAs and mRNAs in COVID-19 patients is not fully understood. The purpose of the present study was to explore this association.</div></div><div><h3>Method</h3><div>We used Transcriptomics data for lncRNAs and mRNAs from the integrated Gene Expression Omnibus (GEO) to identify Differentially Expressed Genes (DEGs) using R software for statistical and data analysis. Then, we carried out Gene Ontology (GO) analysis and constructed a Protein-Protein Interaction (PPI) network to identify interactions between the genes.</div></div><div><h3>Results</h3><div>In this study, we divided samples into four groups and compared Differentially Expressed lncRNAs (DEls) and DEGs. Genes enriched in immune response and cytokine pathways were identified by GO analysis. By considering the protein–protein interaction network, the hub genes were ALAS2, CCL2, AHSP, and IL5.</div></div><div><h3>Conclusion</h3><div>mRNAs and lncRNAs could be used to identify the effects of SARS-CoV-2 on defined parameters (such as gender, main comorbidities in recovery, and treatment stages). Heme/hemoglobin metabolism was enriched in groups 1, 2, and 4, with four common genes (<em>ALAS2</em>, <em>AHSP</em>, <em>HBD</em>, and <em>CA1</em>) that are associated with the immune response to infection. <em>CCL2</em> was enriched in group 3 and its expression was remarkably high in patients with an unfavorable outcome compared to other cases. Also, while both <em>IL-5</em> and <em>ALAS2</em> were enriched in group 4, IL-5 appeared to have no significant role in COVID-19. Overall, we conducted a bioinformatics analysis to predict how mRNAs and lncRNAs interact in patients with different characteristics such as gender, underlying disease, and treatment or recovery stages. mRNAs and lncRNAs can be potential biomarkers to examine the effect of SARS-CoV-2 on defined parameters.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100650"},"PeriodicalIF":2.8,"publicationDate":"2025-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145840794","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 : 2025-12-23DOI: 10.1016/j.jgeb.2025.100651
Xinyou Wang , Xuetong Chen , Nannan Lu , Jiaoyan Zhong , Xinlv Dai , Xia Zhuang , Fengxian Yao , Ruimin Li
Selenium treatment has been shown to enhance plant resilience against both biotic and abiotic stresses; however, whether it can improve citrus resistance to bacterial diseases remains unexplored. In this study, we systematically identified sulfate transporter (Sultr) genes in the Citrus sinensis genome that are involved in selenate uptake. Analysis of gene structure, conserved motifs, and protein domains revealed a high degree of conservation among CsSultrs. Collinearity analysis between C. sinensis and Arabidopsis thaliana Sultr genes suggested possible evolutionary duplication and divergence events. Expression profiling of sulfur-related genes in C. sinensis following infection with Candidatus Liberibacter asiaticus, Xanthomonas citri subsp. citri, and Colletotrichum gloeosporioides showed that CsSULTR3;5 is responsive to pathogen infection. Subcellular localization indicated that CsSULTR3;5 is localized to the cell membrane and other intracellular organelles. Transient expression of CsSULTR3;5 in Nicotiana benthamiana did not affect leaf chlorophyll or carotenoid content. Furthermore, overexpression of CsSULTR3;5 enhanced resistance to citrus canker. These findings provide insight into the mechanisms by which selenium modulates biotic stress responses in citrus.
{"title":"Integrative analysis of sulfate transporters in Citrus sinensis reveals CsSULTR3;5 involved in pathogen stress response","authors":"Xinyou Wang , Xuetong Chen , Nannan Lu , Jiaoyan Zhong , Xinlv Dai , Xia Zhuang , Fengxian Yao , Ruimin Li","doi":"10.1016/j.jgeb.2025.100651","DOIUrl":"10.1016/j.jgeb.2025.100651","url":null,"abstract":"<div><div>Selenium treatment has been shown to enhance plant resilience against both biotic and abiotic stresses; however, whether it can improve citrus resistance to bacterial diseases remains unexplored. In this study, we systematically identified sulfate transporter (Sultr) genes in the <em>Citrus sinensis</em> genome that are involved in selenate uptake. Analysis of gene structure, conserved motifs, and protein domains revealed a high degree of conservation among CsSultrs. Collinearity analysis between <em>C. sinensis</em> and <em>Arabidopsis thaliana</em> Sultr genes suggested possible evolutionary duplication and divergence events. Expression profiling of sulfur-related genes in <em>C. sinensis</em> following infection with <em>Candidatus</em> Liberibacter asiaticus, <em>Xanthomonas citri</em> subsp. <em>citri</em>, and <em>Colletotrichum gloeosporioides</em> showed that <em>CsSULTR3;5</em> is responsive to pathogen infection. Subcellular localization indicated that CsSULTR3;5 is localized to the cell membrane and other intracellular organelles. Transient expression of <em>CsSULTR3;5</em> in <em>Nicotiana benthamiana</em> did not affect leaf chlorophyll or carotenoid content. Furthermore, overexpression of <em>CsSULTR3;5</em> enhanced resistance to citrus canker. These findings provide insight into the mechanisms by which selenium modulates biotic stress responses in citrus.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100651"},"PeriodicalIF":2.8,"publicationDate":"2025-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145840793","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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