Pub Date : 2025-12-19DOI: 10.1016/j.jgeb.2025.100638
Hong Yu , Gang Gary Hao
Human mesenchymal stromal cells (MSC) have garnered significant interest as cell therapy for a multitude of indications. Despite their clinical potential, the development and commercialization of MSC-based products have been hampered by the challenge in scalable production of MSC ex vivo. At present, bioreactor expansion represents the most significant technical hurdle during the MSC manufacturing process. Intrinsic properties of MSCs, e.g. cell senescence, donor heterogeneity, and shear stress-sensitivity lead to suboptimal productivity and inconsistent quality, that often confounded the clinical efficacy readout. Herein we review the key aspects in bioreactor cultivation of MSCs, including the instrument platforms, critical process parameters, process scale-up, downstream and analytics. Cell senescence, the key limitation in ex vivo MSC expansion, was also discussed along with emerging strategies to circumvent the obstacle. Technological improvement and mechanistic understanding of MSC expansion in bioreactors will accelerate the clinical development of MSC as regenerative medicine.
{"title":"Bioreactors expansion of human mesenchymal stromal cell therapies: platforms, parameters, challenges and opportunities","authors":"Hong Yu , Gang Gary Hao","doi":"10.1016/j.jgeb.2025.100638","DOIUrl":"10.1016/j.jgeb.2025.100638","url":null,"abstract":"<div><div>Human mesenchymal stromal cells (MSC) have garnered significant interest as cell therapy for a multitude of indications. Despite their clinical potential, the development and commercialization of MSC-based products have been hampered by the challenge in scalable production of MSC ex vivo. At present, bioreactor expansion represents the most significant technical hurdle during the MSC manufacturing process. Intrinsic properties of MSCs, e.g. cell senescence, donor heterogeneity, and shear stress-sensitivity lead to suboptimal productivity and inconsistent quality, that often confounded the clinical efficacy readout. Herein we review the key aspects in bioreactor cultivation of MSCs, including the instrument platforms, critical process parameters, process scale-up, downstream and analytics. Cell senescence, the key limitation in ex vivo MSC expansion, was also discussed along with emerging strategies to circumvent the obstacle. Technological improvement and mechanistic understanding of MSC expansion in bioreactors will accelerate the clinical development of MSC as regenerative medicine.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100638"},"PeriodicalIF":2.8,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145798137","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 : 2025-12-12DOI: 10.1016/j.jgeb.2025.100635
Yasser M. Taay , Mustafa Taha Mohammed , Ali Hussain Alwan , Ahmad Hussein Ismail
Biogenic gold nanoparticles (AuNPs) were synthesized using broccoli extract to assess their antioxidant activity, wound-healing potential, and selective anticancer effects. Green synthesis with broccoli offers an environmentally friendly way to produce stable and biocompatible nanomaterials. In this study, Brassica oleracea aqueous extract served as both the reducing and capping agent, producing AuNPs with a characteristic surface plasmon resonance peak at 560 nm and a well-defined cubic crystalline structure confirmed by XRD. TEM analysis showed uniformly dispersed, semi-spherical nanoparticles with an average size of 7.5 ± 3.6 nm. The biosynthesized AuNPs exhibited potent antioxidant activity, achieving 91.2 % DPPH scavenging at 100 µg/mL. In vivo tests demonstrated significantly faster wound healing, with approximately 90 % contraction by day 7 compared to 60 % in the control group, supported by histological evidence of increased collagen deposition and complete epithelialization. Moreover, AuNPs showed selective cytotoxicity towards HepG2 cancer cells (IC50 = 53.45 µg/mL) while maintaining over 70 % viability in normal HDF cells. This selectivity likely stems from differences in redox balance and mitochondrial vulnerability between cancer and healthy cells. Overall, the study presents broccoli-mediated AuNPs as multifunctional nanomaterials with potent antioxidant, regenerative, and targeted anticancer properties, highlighting their promising potential in biomedical applications.
{"title":"Broccoli-mediated gold nanoparticles: Eco-friendly synthesis and nano-bio interactions promoting wound healing and targeted cytotoxicity","authors":"Yasser M. Taay , Mustafa Taha Mohammed , Ali Hussain Alwan , Ahmad Hussein Ismail","doi":"10.1016/j.jgeb.2025.100635","DOIUrl":"10.1016/j.jgeb.2025.100635","url":null,"abstract":"<div><div>Biogenic gold nanoparticles (AuNPs) were synthesized using broccoli extract to assess their antioxidant activity, wound-healing potential, and selective anticancer effects. Green synthesis with broccoli offers an environmentally friendly way to produce stable and biocompatible nanomaterials. In this study, <em>Brassica oleracea</em> aqueous extract served as both the reducing and capping agent, producing AuNPs with a characteristic surface plasmon resonance peak at 560 nm and a well-defined cubic crystalline structure confirmed by XRD. TEM analysis showed uniformly dispersed, semi-spherical nanoparticles with an average size of 7.5 ± 3.6 nm. The biosynthesized AuNPs exhibited potent antioxidant activity, achieving 91.2 % DPPH scavenging at 100 µg/mL. <em>In vivo</em> tests demonstrated significantly faster wound healing, with approximately 90 % contraction by day 7 compared to 60 % in the control group, supported by histological evidence of increased collagen deposition and complete epithelialization. Moreover, AuNPs showed selective cytotoxicity towards HepG2 cancer cells (IC<sub>50</sub> = 53.45 µg/mL) while maintaining over 70 % viability in normal HDF cells. This selectivity likely stems from differences in redox balance and mitochondrial vulnerability between cancer and healthy cells. Overall, the study presents broccoli-mediated AuNPs as multifunctional nanomaterials with potent antioxidant, regenerative, and targeted anticancer properties, highlighting their promising potential in biomedical applications.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100635"},"PeriodicalIF":2.8,"publicationDate":"2025-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145749785","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 : 2025-12-09DOI: 10.1016/j.jgeb.2025.100629
Somasundaram Iyyappan, Suvadip Ghara, Irfan Ahmad Bhat, Irfan Ahmad Khan, Mohd Ashraf Rather
The mitochondrial genome serves as a crucial molecular marker for studying phylogenetic relationships and molecular evolution in fish. Despite their ecological significance in freshwater ecosystems, Glyptothorax fishes have limited evolutionary research, with only a few complete mitochondrial genomes reported. The present study examines the complete mitochondrial DNA (mtDNA) of Glyptothorax cavia, G. trilineatus, G. annandalei, G. sinensis, and G. granosus, with sequence lengths of 16,529 base pairs (bp), 16,539 bp, 16,541 bp, 16,531 bp, and 16,540 bp, respectively. Our comprehensive analysis reveals that most protein-coding genes (PCGs) begin with the ATG codon and terminate with the TAA stop codon, although some exhibit incomplete stop codons (T/TA). The majority of the 13 protein-coding genes (PCGs) display a negative guanine-cytosine (GC) skew, except for the (Skew value: 0.53–0.60) NADH dehydrogenase subunit 6 (ND6) gene. In terms of adenine–thymine (AT) (AT Skew value: 0–0.007), eight PCGs have positive values, while cytochrome c oxidase subunit 1 (COX1-), NADH dehydrogenase subunit 3 (ND3), NADH dehydrogenase subunit 4L (ND4L), NADH dehydrogenase subunit 4 (ND4), NADH dehydrogenase subunit 5 (ND5), and cytochrome b (Cytb) exhibit negative values. Genetic distance and non-synonymous to synonymous substitution ratio (Ka/Ks) analyses indicate purifying selection acting on the 13 PCGs, with selection pressures potentially influenced by environmental adaptations. Phylogenetic and evolutionary analyses identify G. sinensis, G. annandalei, and G. granosus as closely related species.
{"title":"Uncovering evolutionary and phylogenetic relationships in Glyptothorax species through comparative mitochondrial genomics","authors":"Somasundaram Iyyappan, Suvadip Ghara, Irfan Ahmad Bhat, Irfan Ahmad Khan, Mohd Ashraf Rather","doi":"10.1016/j.jgeb.2025.100629","DOIUrl":"10.1016/j.jgeb.2025.100629","url":null,"abstract":"<div><div>The mitochondrial genome serves as a crucial molecular marker for studying phylogenetic relationships and molecular evolution in fish. Despite their ecological significance in freshwater ecosystems, <em>Glyptothorax</em> fishes have limited evolutionary research, with only a few complete mitochondrial genomes reported. The present study examines the complete mitochondrial DNA (mtDNA) of <em>Glyptothorax cavia</em>, <em>G. trilineatus</em>, <em>G. annandalei</em>, <em>G. sinensis</em>, and <em>G. granosus</em>, with sequence lengths of 16,529 base pairs (bp), 16,539 bp, 16,541 bp, 16,531 bp, and 16,540 bp, respectively. Our comprehensive analysis reveals that most protein-coding genes (PCGs) begin with the ATG codon and terminate with the TAA stop codon, although some exhibit incomplete stop codons (T/TA). The majority of the 13 protein-coding genes (PCGs) display a negative guanine-cytosine (GC) skew, except for the (Skew value: 0.53–0.60) NADH dehydrogenase subunit 6 (ND6) gene. In terms of adenine–thymine (AT) (AT Skew value: 0–0.007), eight PCGs have positive values, while cytochrome <em>c</em> oxidase subunit 1 (COX1-), NADH dehydrogenase subunit 3 (ND3), NADH dehydrogenase subunit 4L (ND4L), NADH dehydrogenase subunit 4 (ND4), NADH dehydrogenase subunit 5 (ND5), and cytochrome <em>b</em> (Cytb) exhibit negative values. Genetic distance and non-synonymous to synonymous substitution ratio (Ka/Ks) analyses indicate purifying selection acting on the 13 PCGs, with selection pressures potentially influenced by environmental adaptations. Phylogenetic and evolutionary analyses identify <em>G. sinensis</em>, <em>G. annandalei</em>, and <em>G. granosus</em> as closely related species.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100629"},"PeriodicalIF":2.8,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145749784","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 : 2025-12-06DOI: 10.1016/j.jgeb.2025.100631
Jianshuang Shen , Yuanjun Ye , Yiwei Zhou , Xianlin Rong
The genus Rhododendron Linnaeus, comprising over 1,000 species distributed across temperate and alpine regions of Asia, Europe, and North America, holds significant value for its ornamental characteristics, ecological adaptability, and medicinal potential. Despite its importance, the genus presents persistent challenges in taxonomic classification and phylogenetic resolution, compounded by the current insufficiency of genomic SSR markers (g-SSRs) for comprehensive genetic studies. In this study, we conducted the first comprehensive genome-wide identification of SSR markers using whole-genome sequencing data of Rhododendron × pulchrum Sweet. Our analysis identified 324,674 SSR loci across the 509.49 Mb genome. From 190 synthesized primer pairs, 124 (65.3 %) demonstrated successful amplification, with 30 (24.2 %) showing high polymorphism. These polymorphic g-SSR markers generated 597 polymorphic bands, exhibiting polymorphic information content (PIC) values ranging from 0.240 to 0.949 (mean = 0.748), reflecting substantial genetic diversity among the studied accessions. Genetic structure, cluster analysis, and principal coordinates analysis of 96 Rhododendron accessions revealed three distinct clades that correlated with geographic origins, hybrid relationships, and utilization values. Association mapping identified 17 SSR markers significantly linked (P < 0.05) to 10 key morphological traits, explaining 5.68–13.35 % of phenotypic variance. The number of significantly associated markers for each trait was as follows: leaf length (1), remontant (3), corolla lobe shape (2), initial flowering period (3), flower diameter (3), leaf shape (1), petal type (3), petiole length (2), stamen number (4), and flower shape (1). This study provides valuable genomic resources for marker-assisted breeding and establishes a foundation for systematic characterization, conservation, and utilization of Rhododendron genetic resources.
{"title":"Genomic SSR markers elucidate genetic architecture and phenotypic trait associations in Rhododendron Linnaeus","authors":"Jianshuang Shen , Yuanjun Ye , Yiwei Zhou , Xianlin Rong","doi":"10.1016/j.jgeb.2025.100631","DOIUrl":"10.1016/j.jgeb.2025.100631","url":null,"abstract":"<div><div>The genus <em>Rhododendron</em> Linnaeus, comprising over 1,000 species distributed across temperate and alpine regions of Asia, Europe, and North America, holds significant value for its ornamental characteristics, ecological adaptability, and medicinal potential. Despite its importance, the genus presents persistent challenges in taxonomic classification and phylogenetic resolution, compounded by the current insufficiency of genomic SSR markers (g-SSRs) for comprehensive genetic studies. In this study, we conducted the first comprehensive genome-wide identification of SSR markers using whole-genome sequencing data of <em>Rhododendron</em> × <em>pulchrum</em> Sweet. Our analysis identified 324,674 SSR loci across the 509.49 Mb genome. From 190 synthesized primer pairs, 124 (65.3 %) demonstrated successful amplification, with 30 (24.2 %) showing high polymorphism. These polymorphic g-SSR markers generated 597 polymorphic bands, exhibiting polymorphic information content (PIC) values ranging from 0.240 to 0.949 (mean = 0.748), reflecting substantial genetic diversity among the studied accessions. Genetic structure, cluster analysis, and principal coordinates analysis of 96 <em>Rhododendron</em> accessions revealed three distinct clades that correlated with geographic origins, hybrid relationships, and utilization values. Association mapping identified 17 SSR markers significantly linked (<em>P</em> < 0.05) to 10 key morphological traits, explaining 5.68–13.35 % of phenotypic variance. The number of significantly associated markers for each trait was as follows: leaf length (1), remontant (3), corolla lobe shape (2), initial flowering period (3), flower diameter (3), leaf shape (1), petal type (3), petiole length (2), stamen number (4), and flower shape (1). This study provides valuable genomic resources for marker-assisted breeding and establishes a foundation for systematic characterization, conservation, and utilization of <em>Rhododendron</em> genetic resources.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100631"},"PeriodicalIF":2.8,"publicationDate":"2025-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145694617","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 : 2025-12-05DOI: 10.1016/j.jgeb.2025.100632
Manal E. Ahmed , Walaa M. Ibrahim , Reda E.E. Abo El-Fadl , Heba A.M. Abdalla , Yara S Abuhashem , Tamer M. Abd Elaziem
Background
Micropropagation of Papaya (Carica papaya L.) cultivar ’Red Lady’, a commercially the important tropical fruit crop, is a highly efficient biotechnological tool for the mass production of disease-free, genetically uniform, and high-quality planting material compared to conventional propagation methods that cause genetic segregation and disease susceptibility. SCoT is a vital molecular marker for detect genetic stability in plant micropropagation protocols. Accordingly, using SCoT markers to assess genetic stability among carica papaya L. cultivar ‘Red Lady’ plantlets.
Results
The present study aimed to develop an efficient in vitro propagation protocol for papaya using leaves. The highest survival percentage, mean number and length of adventitious buds of papaya leaf segments (97.00 ± 2 %, 119.00 ± 1.53 and 4.8 ± 0.4 cm, respectively) were achieved by using 1.0 mg/l of meta-topoline (mT) after 12 weeks of culture. On the other hand, using 0.5 g/l mT without activated charcoal (AC) showed to give the highest shoot numbers/ explant (73.50 ± 1.0). During rooting stage, using 0.50 mg/l of IBA in combination with NAA at 0.25 mg/l is the most promising treatment that gave the highest significant percentage of rooting (74 ± 2.64 %). In acclimatization stage, 200 ppm silicon (Si) showed to give the most promising results for survival percentage (85 %) that were foliar sprayed and watered acclimatized plantlets with it.
In current study, plantlets obtained by direct organogenesis, eight SCoT markers generated a total of 704 amplicons. Plantlets showed 0.90 genetic uniformity from mother plants during using 8 SCoT markers. These findings strongly support our micropropagation techniques is an vital methodology to generation carica papaya L. cultivar ‘Red Lady’.
Conclusion
Compared with other in vitro propagation methods, direct organogenesis offers a faster and more reliable approach for producing true-to-type papaya plants. This regeneration pathway proved to be efficient, reproducible, and genetically stable, as no somaclonal variation was observed among the regenerated plantlets. Our protocol is controlled and reliable, as adventitious shoots transplanted more than 8 times are consistent with the genetic stability of first-generation donor material. Therefore, Si application can be considered an effective and co-friendly strategy to improve the success rate of acclimatization in tissue cultured plants. The findings of the study proved that there is a significant correlation between physiological parameters (CAT, MDA, stomatal density) and survival percentage.
{"title":"Direct organogenesis and genetic fidelity of papaya ‘Red Lady’ with improved acclimatization using foliar silicon and salicylic acid","authors":"Manal E. Ahmed , Walaa M. Ibrahim , Reda E.E. Abo El-Fadl , Heba A.M. Abdalla , Yara S Abuhashem , Tamer M. Abd Elaziem","doi":"10.1016/j.jgeb.2025.100632","DOIUrl":"10.1016/j.jgeb.2025.100632","url":null,"abstract":"<div><h3>Background</h3><div>Micropropagation of Papaya (<em>Carica papaya</em> L.) cultivar ’Red Lady’, a commercially the important tropical fruit crop, is a highly efficient biotechnological tool for the mass production of disease-free, genetically uniform, and high-quality planting material compared to conventional propagation methods that cause genetic segregation and disease susceptibility. SCoT is a vital molecular marker for detect genetic stability in plant micropropagation protocols. Accordingly, using SCoT markers to assess genetic stability among <em>carica papaya</em> L. cultivar ‘Red Lady’ plantlets.</div></div><div><h3>Results</h3><div>The present study aimed to develop an efficient <em>in vitro</em> propagation protocol for papaya using leaves. The highest survival percentage, mean number and length of adventitious buds of papaya leaf segments (97.00 ± 2 %, 119.00 ± 1.53 and 4.8 ± 0.4 cm, respectively) were achieved by using 1.0 mg/l of <em>meta</em>-topoline (<em>m</em>T) after 12 weeks of culture. On the other hand, using 0.5 g/l <em>m</em>T without activated charcoal (AC) showed to give the highest shoot numbers/ explant (73.50 ± 1.0). During rooting stage, using 0.50 mg/l of IBA in combination with NAA at 0.25 mg/l is the most promising treatment that gave the highest significant percentage of rooting (74 ± 2.64 %). In acclimatization stage, 200 ppm silicon (Si) showed to give the most promising results for survival percentage (85 %) that were foliar sprayed and watered acclimatized plantlets with it.</div><div>In current study, plantlets obtained by direct organogenesis, eight SCoT markers generated a total of 704 amplicons. Plantlets showed 0.90 genetic uniformity from mother plants during using 8 SCoT markers. These findings strongly support our micropropagation techniques is an vital methodology to generation <em>carica papaya</em> L. cultivar ‘Red Lady’.</div></div><div><h3>Conclusion</h3><div>Compared with other <em>in vitro</em> propagation methods, direct organogenesis offers a faster and more reliable approach for producing true-to-type papaya plants. This regeneration pathway proved to be efficient, reproducible, and genetically stable, as no somaclonal variation was observed among the regenerated plantlets. Our protocol is controlled and reliable, as adventitious shoots transplanted more than 8 times are consistent with the genetic stability of first-generation donor material. Therefore, Si application can be considered an effective and co-friendly strategy to improve the success rate of acclimatization in tissue cultured plants. The findings of the study proved that there is a significant correlation between physiological parameters (CAT, MDA, stomatal density) and survival percentage.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100632"},"PeriodicalIF":2.8,"publicationDate":"2025-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145694616","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 : 2025-12-04DOI: 10.1016/j.jgeb.2025.100624
D. Ram Babu , Zakir Hussain , Praveen Kumar Singh , Suman Lata , Alka Joshi , Navinder Saini , T.S. Chaithra
This present study focused on assessing Gamma-aminobutyric acid (GABA) levels in seventy kharif tomato genotypes to highlight its importance in neurotransmission. The experiment was performed at ICAR- Indian Agricultural Research Institute, New Delhi, during 2021–2022. Analysis revealed that most genotypes exhibited a decline in GABA content from the green to turning stages. However, the yellow and orange fruited genotypes K-69 and K-70 consistently maintained stable GABA levels throughout ripening, underscoring their potential for biofortification. In this experiment, efforts were also made to use in-vitro regeneration methods, emphasising proper sterilization technique. Among the different sterilization techniques, NaOCl 2 % for 10 min showed less contamination. Treatment T7 (BAP 2 mg/l, NAA 1.5 mg/l, IBA 0.5 mg/l) was most effective for callus induction, while T5 (BAP 1 mg/l, NAA 0.5 mg/l, IBA 2 mg/l) showed maximum shoot multiplication rate and average number of roots per shoot. Explant length and precise growth regulator combinations were found to be critical factors influencing successful regeneration outcomes. The study encountered challenges such as genotype-dependent variability in tissue culture response and contamination risks, which limited reproducibility across genotypes. Nevertheless, the identification of GABA-stable tomato genotypes and optimized regeneration protocols provides important insights into the relationship between fruit ripening and GABA metabolism. These findings not only advance tissue culture applications for trait improvement and cultivar development but also highlight the nutritional and health benefits of enhancing GABA content in tomato, thereby linking agricultural biotechnology with human health promotion.
{"title":"Gamma-Aminobutyric acid profiling (GABA) and standardization of in-vitro regeneration protocol in tomato (Solanum lycopersicum L.) genotypes","authors":"D. Ram Babu , Zakir Hussain , Praveen Kumar Singh , Suman Lata , Alka Joshi , Navinder Saini , T.S. Chaithra","doi":"10.1016/j.jgeb.2025.100624","DOIUrl":"10.1016/j.jgeb.2025.100624","url":null,"abstract":"<div><div>This present study focused on assessing Gamma-aminobutyric acid (GABA) levels in seventy <em>kharif</em> tomato genotypes to highlight its importance in neurotransmission. The experiment was performed at ICAR- Indian Agricultural Research Institute, New Delhi, during 2021–2022. Analysis revealed that most genotypes exhibited a decline in GABA content from the green to turning stages. However, the yellow and orange fruited genotypes K-69 and K-70 consistently maintained stable GABA levels throughout ripening, underscoring their potential for biofortification. In this experiment, efforts were also made to use <em>in-vitro</em> regeneration methods, emphasising proper sterilization technique. Among the different sterilization techniques, NaOCl 2 % for 10 min showed less contamination. Treatment T<sub>7</sub> (BAP 2 mg/l, NAA 1.5 mg/l, IBA 0.5 mg/l) was most effective for callus induction, while T<sub>5</sub> (BAP 1 mg/l, NAA 0.5 mg/l, IBA 2 mg/l) showed maximum shoot multiplication rate and average number of roots per shoot. Explant length and precise growth regulator combinations were found to be critical factors influencing successful regeneration outcomes. The study encountered challenges such as genotype-dependent variability in tissue culture response and contamination risks, which limited reproducibility across genotypes. Nevertheless, the identification of GABA-stable tomato genotypes and optimized regeneration protocols provides important insights into the relationship between fruit ripening and GABA metabolism. These findings not only advance tissue culture applications for trait improvement and cultivar development but also highlight the nutritional and health benefits of enhancing GABA content in tomato, thereby linking agricultural biotechnology with human health promotion.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"24 1","pages":"Article 100624"},"PeriodicalIF":2.8,"publicationDate":"2025-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145665530","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 : 2025-12-01DOI: 10.1016/j.jgeb.2025.100627
Tianyu Lv , Meiqi Chen , Xixian Li , Yu Long , Yiwen Liang , Tingting Jiang , Jiayi Chen , Yichao Huang , Kailing Guo , Yi Cheng , Zujun Deng , Zhuoya Wang
Silver nanoparticles (AgNPs) are widely used but traditional synthesis methods are energy-intensive and polluting. Biosynthesis offers an eco-friendly approach, yet studies on medicinal plant endophytic fungi remain scarce. This work reports the isolation and characterization of AgNPs synthesized by endophytic fungi from Saxifraga stolonifera, along with an assessment of their bioactivities, including antimicrobial, anticancer, and antioxidant effects. AgNPs were biosynthesized using the aqueous extract of the fungus HECL10, which was identified as Calonectria eucalypti. The HECL10-AgNPs were characterised by UV‒vis spectroscopy, SEM, EDS, TEM, FT-IR and zeta potential analysis. The drug susceptibility experiments illustrated that HECL10-AgNPs exhibited potent antimicrobial activity against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus and Candida albicans. Additionally, the cytotoxicity assays revealed that the HECL10-AgNPs exhibited prominent anticancer effects on the A549, A375, HeLa and HepG2 cell lines. Notably, the scavenging rates of HECL10-AgNPs at 200 µg/mL against DPPH, ABTS, and OH radicals were 90.49 %, 60.38 %, and 38.76 %, respectively. Compared to the H2O2-induced model group, the treatment of HECL10-AgNPs at concentrations of 25.00 µg/mL significantly reduced intracellular ROS levels in HaCaT cells by 44.8 %, and enhanced the activity of SOD, CAT, and GSH by 106.7 %, 2036.1 % and 43.5 %. The results demonstrated that HECL10-AgNPs possessed potent antioxidant properties. These findings revealed the potential for synthesising AgNPs using endophytic fungi from medicinal plants and emphasised the promise of HECL10-AgNPs as a multifunctional nanomedicine for biomedical applications.
{"title":"Silver nanoparticles synthesised using endophytic fungus Calonectria eucalypti from medicinal plant axifraga stolonifera and their bioactivity","authors":"Tianyu Lv , Meiqi Chen , Xixian Li , Yu Long , Yiwen Liang , Tingting Jiang , Jiayi Chen , Yichao Huang , Kailing Guo , Yi Cheng , Zujun Deng , Zhuoya Wang","doi":"10.1016/j.jgeb.2025.100627","DOIUrl":"10.1016/j.jgeb.2025.100627","url":null,"abstract":"<div><div>Silver nanoparticles (AgNPs) are widely used but traditional synthesis methods are energy-intensive and polluting. Biosynthesis offers an eco-friendly approach, yet studies on medicinal plant endophytic fungi remain scarce. This work reports the isolation and characterization of AgNPs synthesized by endophytic fungi from <em>Saxifraga stolonifera</em>, along with an assessment of their bioactivities, including antimicrobial, anticancer, and antioxidant effects. AgNPs were biosynthesized using the aqueous extract of the fungus HECL10, which was identified as <em>Calonectria eucalypti</em>. The HECL10-AgNPs were characterised by UV‒vis spectroscopy, SEM, EDS, TEM, FT-IR and zeta potential analysis. The drug susceptibility experiments illustrated that HECL10-AgNPs exhibited potent antimicrobial activity against <em>Escherichia coli</em>, <em>Pseudomonas aeruginosa</em>, <em>Staphylococcus aureus</em> and <em>Candida albicans</em>. Additionally, the cytotoxicity assays revealed that the HECL10-AgNPs exhibited prominent anticancer effects on the A549, A375, HeLa and HepG2 cell lines. Notably, the scavenging rates of HECL10-AgNPs at 200 µg/mL against DPPH, ABTS, and OH radicals were 90.49 %, 60.38 %, and 38.76 %, respectively. Compared to the H<sub>2</sub>O<sub>2</sub>-induced model group, the treatment of HECL10-AgNPs at concentrations of 25.00 µg/mL significantly reduced intracellular ROS levels in HaCaT cells by 44.8 %, and enhanced the activity of SOD, CAT, and GSH by 106.7 %, 2036.1 % and 43.5 %. The results demonstrated that HECL10-AgNPs possessed potent antioxidant properties. These findings revealed the potential for synthesising AgNPs using endophytic fungi from medicinal plants and emphasised the promise of HECL10-AgNPs as a multifunctional nanomedicine for biomedical applications.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100627"},"PeriodicalIF":2.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145693134","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 : 2025-12-01DOI: 10.1016/j.jgeb.2025.100622
Keying Li , Tuliang Liang , Minfang Li , Xuxin Sun , Wei Xie , Sheng Chen
Background
Chronic obstructive pulmonary disease (COPD) and Helicobacter pylori (H. pylori) infection may share common pathogenic mechanisms, yet their molecular and cellular interactions remain poorly defined.
Methods
Public datasets for COPD and H. pylori infection were retrieved from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified, followed by weighted gene co-expression network analysis (WGCNA) to define disease-associated modules. Overlapping genes underwent functional enrichment via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Support vector machine-recursive feature elimination (SVM-RFE) was analyzed to identify hub genes. Gene set enrichment analysis (GSEA), receiver operating characteristic (ROC) curve validation, and immune infiltration analysis using CIBERSORT were performed. Single-cell RNA sequencing (scRNA-seq) and cell–cell communication analysis were further applied to characterize hub gene expression and intercellular interactions.
Results
Integrative analysis identified 100 co-expressed genes, which were associated with cytokine-receptor interaction, TNF signaling, and chemokine-mediated signaling. SVM-RFE highlighted CCR1 and CCL19 as shared genes, validated in external cohorts, with GSEA indicating involvement in immune and inflammatory signaling. ROC curves confirmed robust diagnostic performance. Immune infiltration analysis showed macrophages M0 were consistently elevated in COPD and H. pylori infection; CCR1 and CCL19 are associated with multiple immune cell types. Single-cell analysis revealed hub genes are primarily expressed in macrophages and fibroblasts, potentially modulating pathogenesis via interactions between immune and signaling pathways.
Conclusion
CCR1 and CCL19 are shared genes linking COPD and H. pylori infetion, which regulate immune homeostasis and inflammatory signaling via influencing macrophages and fibroblasts. These findings offered new ideas for molecular mechanisms and integrated therapeutic interventions in COPD and H. pylori infetion.
背景：慢性阻塞性肺疾病（COPD）和幽门螺杆菌（H. pylori）感染可能具有共同的致病机制，但它们的分子和细胞相互作用尚未明确。方法从Gene Expression Omnibus （GEO）数据库中检索COPD和幽门螺杆菌感染的公共数据集。鉴定差异表达基因（DEGs），然后通过加权基因共表达网络分析（WGCNA）确定疾病相关模块。通过基因本体（GO）和京都基因与基因组百科全书（KEGG）对重叠基因进行功能富集。采用支持向量机递归特征消去法（SVM-RFE）识别轮毂基因。进行基因集富集分析（GSEA）、受试者工作特征（ROC）曲线验证和免疫浸润分析（CIBERSORT）。单细胞RNA测序（scRNA-seq）和细胞间通讯分析进一步用于表征枢纽基因表达和细胞间相互作用。结果整合分析鉴定出100个共表达基因，这些基因与细胞因子受体相互作用、TNF信号传导和趋化因子介导的信号传导有关。SVM-RFE强调CCR1和CCL19是共享基因，在外部队列中得到验证，GSEA表明参与免疫和炎症信号传导。ROC曲线证实了稳健的诊断性能。免疫浸润分析显示，慢性阻塞性肺病和幽门螺杆菌感染中巨噬细胞M0持续升高；CCR1和CCL19与多种免疫细胞类型相关。单细胞分析显示hub基因主要在巨噬细胞和成纤维细胞中表达，可能通过免疫和信号通路之间的相互作用调节发病机制。结论ccr1和CCL19是COPD和幽门螺杆菌感染的共同基因，通过影响巨噬细胞和成纤维细胞调节免疫稳态和炎症信号。这些发现为COPD和幽门螺杆菌感染的分子机制和综合治疗干预提供了新的思路。
{"title":"Hub genes and common pathogenic mechanisms between COPD and H. pylori infection","authors":"Keying Li , Tuliang Liang , Minfang Li , Xuxin Sun , Wei Xie , Sheng Chen","doi":"10.1016/j.jgeb.2025.100622","DOIUrl":"10.1016/j.jgeb.2025.100622","url":null,"abstract":"<div><h3>Background</h3><div>Chronic obstructive pulmonary disease (COPD) and<!--> <em>Helicobacter pylori</em> (<em>H. pylori</em>) infection may share common pathogenic mechanisms, yet their molecular and cellular interactions remain poorly defined.</div></div><div><h3>Methods</h3><div>Public datasets for COPD and <em>H. pylori</em> <!-->infection were retrieved from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified, followed by weighted gene co-expression network analysis (WGCNA) to define disease-associated modules. Overlapping genes underwent functional enrichment via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Support vector machine-recursive feature elimination (SVM-RFE) was analyzed<!--> <!-->to identify hub genes. Gene set enrichment analysis (GSEA), receiver operating characteristic (ROC) curve validation, and immune infiltration analysis using CIBERSORT were performed. Single-cell RNA sequencing (scRNA-seq) and cell–cell communication analysis were further applied to characterize hub gene expression and intercellular interactions.</div></div><div><h3>Results</h3><div>Integrative analysis identified 100 co-expressed genes, which were associated with cytokine-receptor interaction, TNF signaling, and chemokine-mediated signaling.<!--> <!-->SVM-RFE highlighted<!--> <!-->CCR1<!--> <!-->and<!--> <!-->CCL19<!--> <!-->as shared genes, validated in external cohorts, with GSEA indicating involvement in immune and inflammatory signaling.<!--> <!-->ROC curves confirmed robust diagnostic performance.<!--> <!-->Immune infiltration analysis showed macrophages M0 were consistently elevated in COPD and <em>H. pylori</em> infection; CCR1 and CCL19 are associated with multiple immune cell types. Single-cell analysis revealed hub genes are primarily expressed in macrophages and fibroblasts, potentially modulating pathogenesis via interactions between immune and signaling pathways.</div></div><div><h3>Conclusion</h3><div>CCR1 and CCL19 are shared genes linking COPD and <em>H. pylori</em> infetion, which regulate immune homeostasis and inflammatory signaling<!--> <!-->via influencing macrophages<!--> <!-->and fibroblasts. These findings offered new ideas for molecular mechanisms and integrated therapeutic interventions<!--> <!-->in COPD and <em>H. pylori</em> infetion.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100622"},"PeriodicalIF":2.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145623559","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 : 2025-12-01DOI: 10.1016/j.jgeb.2025.100623
Qijun Wu , Sanbao Su , Yuxiao Han , Shuyuan Deng , Bo Wang , Yuehui She , Fan Zhang
Pseudomonas stutzeri is a type of microorganism widely present in nature, particularly in petroleum-contaminated environments, where it exhibits a high capacity for biodegradation. In this study, two strains of Pseudomonas stutzeri 1W1-1A and DW2-1A, were isolated from oil-water samples from Dagang Oilfield and their whole genomes were sequenced. The whole genome of 1W1-1A is 4,454,378 bp in size, with a GC content of 64.23 % in its single circular chromosome; the whole genome of DW2-1A is 3,967,155 bp in size, with a GC content of 62.98 % in its single circular chromosome. Comparing these two strains with Pseudomonas sp. in the NCBI database, we counted the strains with genes related to hydrocarbon oxidation, nitrate, sulfite, and oxygen reduction in the genome and their global distribution. Genes related to hydrocarbon oxidation, nitrate, sulfite, and oxygen reduction were found in the genome, revealing the survival strategies and adaptation mechanisms of Pseudomonas in extreme oil reservoir environments, including its genomic characteristics, functional gene distribution, and tolerance to different environmental conditions. These findings enrich our understanding of the ecological adaptability and functional evolution of Pseudomonas, providing a new perspective for research in microbial ecology and environmental microbiology. The results of this study offer new strain resources and a scientific basis for microbial enhanced oil recovery (MEOR). Utilizing the hydrocarbon degradation capabilities and biosurfactant production characteristics of these strains is of great significance for microbial industrial applications such as MEOR and the remediation of petroleum-contaminated environments.
{"title":"Full genome sequences of two strains of Pseudomonas stutzeri isolated from oil reservoirs and their adaptation mechanisms to harsh environments","authors":"Qijun Wu , Sanbao Su , Yuxiao Han , Shuyuan Deng , Bo Wang , Yuehui She , Fan Zhang","doi":"10.1016/j.jgeb.2025.100623","DOIUrl":"10.1016/j.jgeb.2025.100623","url":null,"abstract":"<div><div><em>Pseudomonas stutzeri</em> is a type of microorganism widely present in nature, particularly in petroleum-contaminated environments, where it exhibits a high capacity for biodegradation. In this study, two strains of <em>Pseudomonas stutzeri</em> 1W1-1A and DW2-1A, were isolated from oil-water samples from Dagang Oilfield and their whole genomes were sequenced. The whole genome of 1W1-1A is 4,454,378 bp in size, with a GC content of 64.23 % in its single circular chromosome; the whole genome of DW2-1A is 3,967,155 bp in size, with a GC content of 62.98 % in its single circular chromosome. Comparing these two strains with <em>Pseudomonas</em> sp. in the NCBI database, we counted the strains with genes related to hydrocarbon oxidation, nitrate, sulfite, and oxygen reduction in the genome and their global distribution. Genes related to hydrocarbon oxidation, nitrate, sulfite, and oxygen reduction were found in the genome, revealing the survival strategies and adaptation mechanisms of <em>Pseudomonas</em> in extreme oil reservoir environments, including its genomic characteristics, functional gene distribution, and tolerance to different environmental conditions. These findings enrich our understanding of the ecological adaptability and functional evolution of <em>Pseudomonas</em>, providing a new perspective for research in microbial ecology and environmental microbiology. The results of this study offer new strain resources and a scientific basis for microbial enhanced oil recovery (MEOR). Utilizing the hydrocarbon degradation capabilities and biosurfactant production characteristics of these strains is of great significance for microbial industrial applications such as MEOR and the remediation of petroleum-contaminated environments.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100623"},"PeriodicalIF":2.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145623560","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}
Forensic DNA typing has become widely accepted in criminal investigations, familial relationship testing, and identification. This process currently relies on the analysis of short tandem repeat (STR) markers. This is because DNA profiling serves as a highly effective means of identifying individuals on the basis of their distinct genetic characteristics. DNA evidence can also be utilized to clear innocent suspects of any wrongdoing. Recent technological advancements in DNA profiling, such as the implementation of statistical methods, have increased the precision of this tool in forensic investigations.
Objective
The main objective of this study was to evaluate the forensic efficiency parameters of the D13S317 marker in closely related family members in Gondar town, Northwest Ethiopia.
Methods
To conduct this study, 87 blood samples were collected in EDTA tubes from various kebeles in Gondar town between October and December 2024. DNA was extracted via the salting-out method, and PCR amplification was performed with forward and reverse primers. After amplification, the PCR products were analyzed on a 1.8 % agarose gel and visualized with a gel documentation system.
Results
The discrimination power, random match probability, typical paternity index, polymorphism information content, and genetic diversity of the D13S317 marker were 0.77, 0.232, 0.5, 0.73 and 0.77, respectively. Five alleles were also confirmed, with the 192 bp allele exhibiting the highest frequency at 33 %, whereas the 176 bp allele had the lowest frequency at 5.7 %.
Conclusion
The D13S317 marker has average discrimination power, making it a valuable tool for DNA profiling, paternity testing, and population genetics studies.
{"title":"Evaluate the forensic efficiency parameters of the D13S317 gene in closely related family members in Gondar town, Northwest Ethiopia","authors":"Betelhem Abebe Begashew , Temesgen Mitiku Yeshanew , Wagaw sendeku , Nega Birhane","doi":"10.1016/j.jgeb.2025.100628","DOIUrl":"10.1016/j.jgeb.2025.100628","url":null,"abstract":"<div><h3>Background</h3><div>Forensic DNA typing has become widely accepted in criminal investigations, familial relationship testing, and identification. This process currently relies on the analysis of short tandem repeat (STR) markers. This is because DNA profiling serves as a highly effective means of identifying individuals on the basis of their distinct genetic characteristics. DNA evidence can also be utilized to clear innocent suspects of any wrongdoing. Recent technological advancements in DNA profiling, such as the implementation of statistical methods, have increased the precision of this tool in forensic investigations.</div></div><div><h3>Objective</h3><div>The main objective of this study was to evaluate the forensic efficiency parameters of the <em>D13S317</em> marker in closely related family members in Gondar town, Northwest Ethiopia.</div></div><div><h3>Methods</h3><div>To conduct this study, 87 blood samples were collected in EDTA tubes from various kebeles in Gondar town between October and December 2024. DNA was extracted via the salting-out method, and PCR amplification was performed with forward and reverse primers. After amplification, the PCR products were analyzed on a 1.8 % agarose gel and visualized with a gel documentation system.</div></div><div><h3>Results</h3><div>The discrimination power, random match probability, typical paternity index, polymorphism information content, and genetic diversity of the D13S317 marker were 0.77, 0.232, 0.5, 0.73 and 0.77, respectively. Five alleles were also confirmed, with the 192 bp allele exhibiting the highest frequency at 33 %, whereas the 176 bp allele had the lowest frequency at 5.7 %.</div></div><div><h3>Conclusion</h3><div>The D13S317 marker has average discrimination power, making it a valuable tool for DNA profiling, paternity testing, and population genetics studies.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100628"},"PeriodicalIF":2.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145693247","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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