Pub Date : 2025-10-21DOI: 10.1016/j.jgeb.2025.100587
Thi Van Anh Tran , Thuy Hang Dam , Lan Huong Nguyen , Tuan Le , Thi Kieu Oanh Vu , Thomas Walther , Ha Thanh Le
Chitin is found in tremendous quantities in nature, especially in the marine environment. This polymer has a stable structure that requires a relatively long time to degrade. As a result, fast-growing microorganisms capable of degrading chitin might be a potential approach in responding to the hydrolysis of this abundant material. This study focused on the isolation of chitinolytic fast-growing bacteria from marine environment in Vietnam, determined their biochemical characteristics, and generally evaluated the relationship between the presence of some important chitinase genes (mostly extracellular) and chitin degradation capacity of the isolates. Crucial chitinase genes were detected via PCR using degenerate primers, while chitin hydrolysis ability was determined via enzymatic measurements, assessing strains’ growth on chitin and chitin hydrolysate composition. The results showed that fourteen chitinolytic fast-growing bacteria isolated from seawater in Vietnam belonged to the family Vibrionaceae and the majority of them possessed all five tested chitinase genes including VCA0027 (chitinase), VC1952 (endochitinase), VC0769 (endochitinase), VCA0700 (chitodextrinase), VC2217 (hexosaminidase). V. natriegens isolates N5.3, N7.2, and 10.3, which lack VC1952 and VC0769, exhibited significantly reduced enzymatic activities, weak chitin hydrolysis, and limited growth on chitin substrates, highlighting the crucial role of these genes for efficient chitin degradation.
{"title":"Isolation and characterization of chitinolytic fast-growing bacteria from marine environment in Vietnam","authors":"Thi Van Anh Tran , Thuy Hang Dam , Lan Huong Nguyen , Tuan Le , Thi Kieu Oanh Vu , Thomas Walther , Ha Thanh Le","doi":"10.1016/j.jgeb.2025.100587","DOIUrl":"10.1016/j.jgeb.2025.100587","url":null,"abstract":"<div><div>Chitin is found in tremendous quantities in nature, especially in the marine environment. This polymer has a stable structure that requires a relatively long time to degrade. As a result, fast-growing microorganisms capable of degrading chitin might be a potential approach in responding to the hydrolysis of this abundant material. This study focused on the isolation of chitinolytic fast-growing bacteria from marine environment in Vietnam, determined their biochemical characteristics, and generally evaluated the relationship between the presence of some important chitinase genes (mostly extracellular) and chitin degradation capacity of the isolates. Crucial chitinase genes were detected via PCR using degenerate primers, while chitin hydrolysis ability was determined via enzymatic measurements, assessing strains’ growth on chitin and chitin hydrolysate composition. The results showed that fourteen chitinolytic fast-growing bacteria isolated from seawater in Vietnam belonged to the family <em>Vibrionaceae</em> and the majority of them possessed all five tested chitinase genes including <em>VCA0027</em> (chitinase), <em>VC1952</em> (endochitinase), <em>VC0769</em> (endochitinase), <em>VCA0700</em> (chitodextrinase), <em>VC2217</em> (hexosaminidase). <em>V. natriegens</em> isolates N5.3, N7.2, and 10.3, which lack VC1952 and VC0769, exhibited significantly reduced enzymatic activities, weak chitin hydrolysis, and limited growth on chitin substrates, highlighting the crucial role of these genes for efficient chitin degradation.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100587"},"PeriodicalIF":2.8,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145362168","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 : 2025-10-21DOI: 10.1016/j.jgeb.2025.100598
Sujuan Li , Huijuan Wang , Yuanhang Zhang
Objective
This article aims to evaluate the role of factors associated with oxidative stress induction in fluctuating hyperglycemia-induced diabetic kidney disease (DKD) and to elucidate the molecular mechanisms underlying the pathogenesis of DKD.
Methods
We downloaded the gene expression datasets GSE30528 and GSE30529, which are associated with diabetic kidney disease (DKD), from the Gene Expression Omnibus (GEO) database. We identified differentially expressed genes (DEGs) and selected the top four proteins from protein-protein interaction (PPI) networks using STRING and Cytoscape software. Concurrently, we conducted diabetic animal experiments to verify that these proteins contribute to the onset and progression of DKD through oxidative stress. Finally, we confirmed the correlation and roles of these genes in the animal model.
Result
The modulation of the MAPK cascade involves ITGB2 and TYROBP. The results showed that the areas under the ROC curve (AUC) for TYROBP were 0.889 and 0.966, respectively, while for ITGB2, they were 0.906 and 0.974. All other indicators had an AUC of 1.0; these indicators represent differentially expressed genes identified through data analysis. The activities of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px), as well as the levels of malondialdehyde (MDA), were measured in diabetic rats (P < 0.05). Apoptotic responses and c-Jun N-terminal kinase (JNK) activation were evident in the rat fluctuation group. Further research has demonstrated that oxidative stress regulates the MAPK pathway at both cellular and molecular levels. Gene and protein expression, particularly in the context of diabetic nephropathy, are influenced by multiple factors.
Conclusion
Collectively, fluctuating hyperglycemia directly and indirectly regulates MAPK-JNK signaling via ITGB2, TYROBP, and oxidative stress, ultimately influencing the onset and progression of diabetic nephropathy.
目的探讨氧化应激诱导相关因子在波动高血糖诱导的糖尿病肾病（DKD）中的作用，并阐明DKD发病的分子机制。方法从gene expression Omnibus （GEO）数据库中下载与糖尿病肾病（DKD）相关的基因表达数据集GSE30528和GSE30529。我们使用STRING和Cytoscape软件鉴定了差异表达基因（DEGs），并从蛋白-蛋白相互作用（PPI）网络中选择了前四个蛋白。同时，我们进行了糖尿病动物实验，以验证这些蛋白通过氧化应激参与DKD的发生和进展。最后，我们在动物模型中证实了这些基因的相关性和作用。结果MAPK级联的调控涉及ITGB2和TYROBP。结果表明，TYROBP的ROC曲线下面积（AUC）分别为0.889和0.966，ITGB2的AUC分别为0.906和0.974。其他指标的AUC均为1.0；这些指标代表通过数据分析鉴定出的差异表达基因。测定糖尿病大鼠血清超氧化物歧化酶（SOD）、谷胱甘肽过氧化物酶（GSH-Px）活性及丙二醛（MDA）水平（P < 0.05）。波动组大鼠出现明显的凋亡反应和c-Jun n -末端激酶（JNK）活化。进一步的研究表明，氧化应激在细胞和分子水平上调控MAPK通路。基因和蛋白的表达，特别是在糖尿病肾病的情况下，受到多种因素的影响。综上所示，波动型高血糖通过ITGB2、TYROBP和氧化应激直接或间接调节MAPK-JNK信号，最终影响糖尿病肾病的发生和进展。
{"title":"Bioinformatics and experimental validation of MAPK pathway activation in diabetic kidney disease induced by glucose variability","authors":"Sujuan Li , Huijuan Wang , Yuanhang Zhang","doi":"10.1016/j.jgeb.2025.100598","DOIUrl":"10.1016/j.jgeb.2025.100598","url":null,"abstract":"<div><h3>Objective</h3><div>This article aims to evaluate the role of factors associated with oxidative stress induction in fluctuating hyperglycemia-induced diabetic kidney disease (DKD) and to elucidate the molecular mechanisms underlying the pathogenesis of DKD.</div></div><div><h3>Methods</h3><div>We downloaded the gene expression datasets GSE30528 and GSE30529, which are associated with diabetic kidney disease (DKD), from the Gene Expression Omnibus (GEO) database. We identified differentially expressed genes (DEGs) and selected the top four proteins from protein-protein interaction (PPI) networks using STRING and Cytoscape software. Concurrently, we conducted diabetic animal experiments to verify that these proteins contribute to the onset and progression of DKD through oxidative stress. Finally, we confirmed the correlation and roles of these genes in the animal model.</div></div><div><h3>Result</h3><div>The modulation of the MAPK cascade involves ITGB2 and TYROBP. The results showed that the areas under the ROC curve (AUC) for TYROBP were 0.889 and 0.966, respectively, while for ITGB2, they were 0.906 and 0.974. All other indicators had an AUC of 1.0; these indicators represent differentially expressed genes identified through data analysis. The activities of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px), as well as the levels of malondialdehyde (MDA), were measured in diabetic rats (P < 0.05). Apoptotic responses and c-Jun N-terminal kinase (JNK) activation were evident in the rat fluctuation group. Further research has demonstrated that oxidative stress regulates the MAPK pathway at both cellular and molecular levels. Gene and protein expression, particularly in the context of diabetic nephropathy, are influenced by multiple factors.</div></div><div><h3>Conclusion</h3><div>Collectively, fluctuating hyperglycemia directly and indirectly regulates MAPK-JNK signaling via ITGB2, TYROBP, and oxidative stress, ultimately influencing the onset and progression of diabetic nephropathy.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100598"},"PeriodicalIF":2.8,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145362167","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 : 2025-10-18DOI: 10.1016/j.jgeb.2025.100588
Yuan Ping , Toporova Viktoriia , Lin Baohang , Argentova Victoria
IgA antibodies have great potential for use in novel cancer immunotherapy based on recombinant monoclonal antibodies. This antitumor application is related to the effector functions of IgA. IgA subisotypes have special effector function features explained by a more complex glycosylation process compared to IgG antibodies. Studying of interrelations of metabolites, glucose consumptions, cell growth and antibody production can allow to get better control of antibody glycosylation and product quality. Reducing of metabolites in culture have influence on productivity and probably on glycosylation and can be achieved through process optimization or metabolic engineering. IgA1 and IgA2m1 have different effector functions associated with distinct glycosylation profiles. The aim of our study was to evaluate the effect of human growth factors such as hNGF, hEGF, and FGF-b combined with some supplements on metabolic level and production of recombinant IgA antibodies. The results demonstrated that combination growth factors and succinic acid improves metabolism of CHO cells producing recombinant monoclonal antibody IgA isotype, especially for IgA2m1producing cell line. These results suggest that combining hNGF, hEGF, and succinic acid supplementation has the potential to be used as effective additives to cell media for increasing the cell culture density, and optimization of IgA1-IgA2 cell line productivity.
{"title":"Influence of growth factors and different supplements on metabolic response and productivity of IgA-producing CHO cell lines","authors":"Yuan Ping , Toporova Viktoriia , Lin Baohang , Argentova Victoria","doi":"10.1016/j.jgeb.2025.100588","DOIUrl":"10.1016/j.jgeb.2025.100588","url":null,"abstract":"<div><div>IgA antibodies have great potential for use in novel cancer immunotherapy based on recombinant monoclonal antibodies. This antitumor application is related to the effector functions of IgA. IgA subisotypes have special effector function features explained by a more complex glycosylation process compared to IgG antibodies. Studying of interrelations of metabolites, glucose consumptions, cell growth and antibody production can allow to get better control of antibody glycosylation and product quality. Reducing of metabolites in culture have influence on productivity and probably on glycosylation and can be achieved through process optimization or metabolic engineering. IgA1 and IgA2m1 have different effector functions associated with distinct glycosylation profiles. The aim of our study was to evaluate the effect of human growth factors such as hNGF, hEGF, and FGF-b combined with some supplements on metabolic level and production of recombinant IgA antibodies. The results demonstrated that combination growth factors and succinic acid improves metabolism of CHO cells producing recombinant monoclonal antibody IgA isotype, especially for IgA2m1producing cell line. These results suggest that combining hNGF, hEGF, and succinic acid supplementation has the potential to be used as effective additives to cell media for increasing the cell culture density, and optimization of IgA1-IgA2 cell line productivity.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100588"},"PeriodicalIF":2.8,"publicationDate":"2025-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145332245","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 : 2025-10-18DOI: 10.1016/j.jgeb.2025.100599
Raúl Vargas, Carmen N. Vigo, Marly Guelac, Eyner Huaman, Manuel Oliva-Cruz
Physalis peruviana L. (known as aguaymanto or goldenberry) is a high-value Andean fruit crop with growing international demand due to its nutritional and nutraceutical properties. However, the development of advanced biotechnological tools for this species has been limited by the lack of efficient and reproducible in vitro regeneration protocols. Existing systems rely primarily on the use of zeatin, a highly effective but expensive cytokinin, which restricts their applicability in resource-limited laboratories. In this study, the synergistic effect of 6-benzylaminopurine (BAP) and meta-topolin (mT) on adventitious shoot regeneration from cotyledonary explants of P. peruviana was evaluated. An initial cytokinin screening identified BAP + mT as the most promising combination, and subsequent optimization revealed that the combination of 9.12 µM BAP with 2.28 µM mT promoted the highest shoot regeneration rate (62.96 %), outperforming previously reported zeatin-based protocols. This treatment also significantly enhanced shoot elongation and rhizogenesis without inducing morphological abnormalities. These results position the BAP + mT combination as an economically viable alternative to replace the use of zeatin in regeneration protocols, with potential applications in genetic transformation programs, in vitro propagation, and the improvement of species in the genus Physalis.
{"title":"Efficient and cost-effective shoot regeneration in Aguaymanto (Physalis peruviana L.) using meta-Topolin and 6-benzylaminopurine combinations","authors":"Raúl Vargas, Carmen N. Vigo, Marly Guelac, Eyner Huaman, Manuel Oliva-Cruz","doi":"10.1016/j.jgeb.2025.100599","DOIUrl":"10.1016/j.jgeb.2025.100599","url":null,"abstract":"<div><div><em>Physalis peruviana</em> L. (known as aguaymanto or goldenberry) is a high-value Andean fruit crop with growing international demand due to its nutritional and nutraceutical properties. However, the development of advanced biotechnological tools for this species has been limited by the lack of efficient and reproducible <em>in vitro</em> regeneration protocols. Existing systems rely primarily on the use of zeatin, a highly effective but expensive cytokinin, which restricts their applicability in resource-limited laboratories. In this study, the synergistic effect of 6-benzylaminopurine (BAP) and meta-topolin (mT) on adventitious shoot regeneration from cotyledonary explants of <em>P. peruviana</em> was evaluated. An initial cytokinin screening identified BAP + mT as the most promising combination, and subsequent optimization revealed that the combination of 9.12 µM BAP with 2.28 µM mT promoted the highest shoot regeneration rate (62.96 %), outperforming previously reported zeatin-based protocols. This treatment also significantly enhanced shoot elongation and rhizogenesis without inducing morphological abnormalities. These results position the BAP + mT combination as an economically viable alternative to replace the use of zeatin in regeneration protocols, with potential applications in genetic transformation programs, <em>in vitro</em> propagation, and the improvement of species in the genus <em>Physalis</em>.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100599"},"PeriodicalIF":2.8,"publicationDate":"2025-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145332244","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 : 2025-10-17DOI: 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":"2025-10-17","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 : 2025-10-17DOI: 10.1016/j.jgeb.2025.100590
Hao Wan , Xutang Tu , Xiaohua Duan , Jun Luo , Zhengrong Zou , Shangguang Du
Heat shock proteins (HSPs) play a crucial role in plant thermotolerance responses. While the regulatory mechanisms of HSPs in Manihot esculenta have been extensively studied, current understanding of the HSP90 gene family, which serves as key regulators in high-temperature adaptation, remains limited in M. esculenta research. HSP90 not only influences M. esculenta growth and development but also significantly affects starch content, ultimately impacting yield. In this study, we identified and characterized 11 HSP90 genes in the M. esculenta genome, which are randomly distributed across seven chromosomes. These genes contain 10 conserved motifs and exhibit variable intron numbers (1–19), suggesting their broad involvement in regulatory networks. Phylogenetic analysis revealed high homology between M. esculenta HSP90 genes and those in Solanum tuberosum. Quantitative real-time PCR demonstrated distinct expression patterns of HSP90 genes under 43 °C heat stress, with significant tissue-specific variations. These findings address a critical knowledge gap by elucidating the cascade effects of HSP90 within the HSP family. Importantly, our results not only clarify the unique regulatory role of HSP90 in M. esculenta ’s heat stress response but also reveal its molecular mechanism in high temperature adaptation through starch biosynthesis regulation, providing valuable molecular targets and theoretical foundations for developing heat-tolerant M. esculenta cultivars.
{"title":"Genome-wide identification and expression analyses of HSP90 genes in cassava (Manihot esculenta)","authors":"Hao Wan , Xutang Tu , Xiaohua Duan , Jun Luo , Zhengrong Zou , Shangguang Du","doi":"10.1016/j.jgeb.2025.100590","DOIUrl":"10.1016/j.jgeb.2025.100590","url":null,"abstract":"<div><div>Heat shock proteins (HSPs) play a crucial role in plant thermotolerance responses. While the regulatory mechanisms of HSPs in <em>Manihot esculenta</em> have been extensively studied, current understanding of the <em>HSP90</em> gene family, which serves as key regulators in high-temperature adaptation, remains limited in <em>M. esculenta</em> research. <em>HSP90</em> not only influences <em>M. esculenta</em> growth and development but also significantly affects starch content, ultimately impacting yield. In this study, we identified and characterized 11 <em>HSP90</em> genes in the <em>M. esculenta</em> genome, which are randomly distributed across seven chromosomes. These genes contain 10 conserved motifs and exhibit variable intron numbers (1–19), suggesting their broad involvement in regulatory networks. Phylogenetic analysis revealed high homology between <em>M. esculenta HSP90</em> genes and those in <em>Solanum tuberosum</em>. Quantitative real-time PCR demonstrated distinct expression patterns of <em>HSP90</em> genes under 43 °C heat stress, with significant tissue-specific variations. These findings address a critical knowledge gap by elucidating the cascade effects of <em>HSP90</em> within the <em>HSP</em> family. Importantly, our results not only clarify the unique regulatory role of <em>HSP90</em> in <em>M. esculenta</em> ’s heat stress response but also reveal its molecular mechanism in high temperature adaptation through starch biosynthesis regulation, providing valuable molecular targets and theoretical foundations for developing heat-tolerant <em>M. esculenta</em> cultivars.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100590"},"PeriodicalIF":2.8,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145332235","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 : 2025-10-16DOI: 10.1016/j.jgeb.2025.100580
Neemat M. Kassem , Mohamed G. Seadawy , Maha Gaafar , Hebatallah A. Kassem , Amira Farouk Ahmed Hussein , Enas M. Ali Rizk , Marwa A. Hassan , Riham H. AbdelAziz , Mentallah M. Abdelradi , Mostafa F. El-Hosseny , Mohamed Abdulla , Rabab Abdel Moneim
Introduction
Colorectal cancer (CRC) is a molecularly diverse disorder arising from gradual accumulation of genetic and epigenetic changes giving interest in characterization of genetic alterations and microsatellite instability (MSI) for identification of new personalized therapeutic targets.
Objectives
Evaluating the incidence of somatic mutations in clinically relative signaling pathways involved in CRC tumorigenesis that include mainly Wnt and MAPK pathways together with MSI and gut microbiota.
Methods
Twenty four CRC patients were enrolled in the study. Cancer hotspot V2 panel was tested using targeted NGS on MiSeqDx device in addition to MSI identification, also gut microbiota was detected using conventional techniques. Patients received FOLFOX regimen in addition to Xeloda especially in early stages.
Results
Non-synonymous genetic variants were detected inTP53, PIK3CA, KDR, KIT, APC, FGFR3 and MET. Twelve patients (50%) had MSI-LO, 25% had MSI-HI and 20.8% were MSS. Missense mutations in PIK3CA, TP53, and KDR were identified in 2, 3, and 2 patients with MSI-HI status, respectively.
In MSI-LO, missense alterations in PIK3CA, TP53, KIT, and KDR were detected in (6, 11, 3, 2 cases, respectively). More than 50% of examined patients revealed mixed GIT flora, 18.8% of patients had E. Coli, 12.5% of patients showed Klebsiella spp. and only 6.3 % of patient revealed Proteus spp. H. pylori antigen was detected in 37.5%of patients and Blastocystis hominis cysts in only 4 patients.
Conclusion
CRC genetic mutational statuses as well as contributing environmental stress factors such as gut microbiota dysbiosis are prognostically crucial, associated with high risk potential of gene-environment interactions based on machine learning.
{"title":"Identifying actionable genetic mutations and microsatellite instability in liquid biopsy of colorectal cancer","authors":"Neemat M. Kassem , Mohamed G. Seadawy , Maha Gaafar , Hebatallah A. Kassem , Amira Farouk Ahmed Hussein , Enas M. Ali Rizk , Marwa A. Hassan , Riham H. AbdelAziz , Mentallah M. Abdelradi , Mostafa F. El-Hosseny , Mohamed Abdulla , Rabab Abdel Moneim","doi":"10.1016/j.jgeb.2025.100580","DOIUrl":"10.1016/j.jgeb.2025.100580","url":null,"abstract":"<div><h3>Introduction</h3><div>Colorectal cancer (CRC) is a molecularly diverse disorder arising from gradual accumulation of genetic and epigenetic changes giving interest in characterization of genetic alterations and microsatellite instability (MSI) for identification of new personalized therapeutic targets.</div></div><div><h3>Objectives</h3><div>Evaluating the incidence of somatic mutations in clinically relative signaling pathways involved in CRC tumorigenesis that include mainly Wnt and MAPK pathways together with MSI and gut microbiota.</div></div><div><h3>Methods</h3><div>Twenty four CRC patients were enrolled in the study. Cancer hotspot V2 panel was tested using targeted NGS on MiSeqDx device in addition to MSI identification, also gut microbiota was detected using conventional techniques. Patients received FOLFOX regimen in addition to Xeloda especially in early stages.</div></div><div><h3>Results</h3><div>Non-synonymous genetic variants were detected in<em>TP53</em>, <em>PIK3CA</em>, <em>KDR</em>, <em>KIT</em>, <em>APC</em>, <em>FGFR3</em> and <em>MET</em>. Twelve patients (50%) had MSI-LO, 25% had MSI-HI and 20.8% were MSS. Missense mutations in PIK3CA, TP53, and KDR were identified in 2, 3, and 2 patients with MSI-HI status, respectively.</div><div>In MSI-LO, missense alterations in PIK3CA, TP53, KIT, and KDR were detected in (6, 11, 3, 2 cases, respectively). More than 50% of examined patients revealed mixed GIT flora, 18.8% of patients had E. Coli, 12.5% of patients showed Klebsiella spp. and only 6.3 % of patient revealed Proteus spp. <strong>H. pylori</strong> antigen was detected in <strong>37.5%</strong>of patients and Blastocystis hominis cysts in only 4 patients.</div></div><div><h3>Conclusion</h3><div>CRC genetic mutational statuses as well as contributing environmental stress factors such as gut microbiota dysbiosis are prognostically crucial, associated with high risk potential of gene-environment interactions based on machine learning.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100580"},"PeriodicalIF":2.8,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145332242","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}
L-arginase-based enzyme therapy, which depletes L-arginine by converting it to L-ornithine and urea, selectively inhibits the growth of L-arginine-dependent cancer cells with low toxicity. This approach shows promise as a novel cancer treatment. This research used Response Surface Methodology (RSM) to enhance L-arginase production by Alcaligenes aquatilis BC2, which was isolated from an Ethiopian soda lake. The Plackett-Burman Design was used to screen eight factors that influence L-arginase production and identified arginine concentration, peptone concentration, and incubation temperature as the most significant variables. The central composite design analysis demonstrated that the optimized conditions of 1.75 % L-arginine concentration, 3 % peptone concentration, and an incubation temperature of 37.5 °C enhance L-arginase production from a baseline of 92.45 U/mL to an optimized yield of 288.79 U/mL. This represents a 3.1-fold increase under the optimized conditions.
The model was developed based on 20 experimental runs, demonstrating excellent fit with R2 = 0.9974 and a significant F-value of 420.28 (p < 0.0001). Additionally, the lack-of-fit test was conducted and found to be non-significant (F-value = 4.18, p = 0.0714), further supporting the model’s predictive strength. This investigation showed that applying statistical design to optimize fermentation conditions leads to increased production of L-arginase, thereby advancing enzyme-based therapeutic practices and highlighting statistical optimization as essential for bioprocess development.
{"title":"Optimization of fermentation conditions for enhanced L-arginase production by Alcaligenes aquatilis BC2 using response surface methodology","authors":"Birhan Getie Assega , Kefyalew Ayalew Getahun , Tamene Milkessa Jiru , Tsehayneh Geremew Yohannes , Mulugeta Aemero , Berhanu Andualem","doi":"10.1016/j.jgeb.2025.100591","DOIUrl":"10.1016/j.jgeb.2025.100591","url":null,"abstract":"<div><div>L-arginase-based enzyme therapy, which depletes L-arginine by converting it to L-ornithine and urea, selectively inhibits the growth of L-arginine-dependent cancer cells with low toxicity. This approach shows promise as a novel cancer treatment. This research used Response Surface Methodology (RSM) to enhance L-arginase production by <em>Alcaligenes aquatilis</em> BC2, which was isolated from an Ethiopian soda lake. The Plackett-Burman Design was used to screen eight factors that influence L-arginase production and identified arginine concentration, peptone concentration, and incubation temperature as the most significant variables. The central composite design analysis demonstrated that the optimized conditions of 1.75 % L-arginine concentration, 3 % peptone concentration, and an incubation temperature of 37.5 °C enhance L-arginase production from a baseline of 92.45 U/mL to an optimized yield of 288.79 U/mL. This represents a 3.1-fold increase under the optimized conditions.</div><div>The model was developed based on 20 experimental runs, demonstrating excellent fit with R2 = 0.9974 and a significant F-value of 420.28 (p < 0.0001). Additionally, the lack-of-fit test was conducted and found to be non-significant (F-value = 4.18, p = 0.0714), further supporting the model’s predictive strength. This investigation showed that applying statistical design to optimize fermentation conditions leads to increased production of L-arginase, thereby advancing enzyme-based therapeutic practices and highlighting statistical optimization as essential for bioprocess development.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100591"},"PeriodicalIF":2.8,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145332238","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":"2025-10-15","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}
Sucrose transporters (SUTs) mediate sucrose movement across plant membranes, playing a crucial role in carbon allocation and stress responses. Although finger millet (Eleusine coracana) is known for its inherent drought resistance, the specific involvement of SUT genes in this characteristic is still unclear. This study aimed to identify the SUT genes of millet and to assess their expression in drought conditions. Five SUT genes (EcSUT1-EcSUT5) were identified that encode proteins with 9–12 transmembrane domains. Phylogenetic analysis clustered these SUT members across all three main SUT groups, suggesting an evolutionary divergence within the family. Synteny analysis revealed conserved genomic regions, with EcSUT2 showing 91–94% identity with orthologs in closely related grasses. Structural models further confirmed their typical transmembrane architecture. Interaction analysis identified EcSUT2 as a key interaction with SWEET transporters. Furthermore, the promoter regions of EcSUT2 and EcSUT5 were found to be enriched with hormone and stress-responsive elements. Under drought conditions, EcSUT1-EcSUT4 displayed transient induction, while EcSUT5 showed sustained upregulation, especially in the roots, notably after 48 h. The finger millet SUT family exhibits evolutionary conservation within grasses, with individual genes that play different roles in stress response. The persistent upregulation of EcSUT5 under drought strongly suggests its involvement in maintaining sucrose transport during long-term adverse conditions. This candidate gene requires further functional validation to uncover the stress dynamics for sustainable crop improvement.
{"title":"Genome-wide identification and evolutionary analysis of SUT genes reveals key regulators of drought stress response in finger millet (Eleusine coracana)","authors":"Kasinathan Rakkammal , Pandiyan Muthuramalingam , Hyunsuk Shin , Manikandan Ramesh","doi":"10.1016/j.jgeb.2025.100592","DOIUrl":"10.1016/j.jgeb.2025.100592","url":null,"abstract":"<div><div>Sucrose transporters (SUTs) mediate sucrose movement across plant membranes, playing a crucial role in carbon allocation and stress responses. Although finger millet (<em>Eleusine coracana</em>) is known for its inherent drought resistance, the specific involvement of <em>SUT</em> genes in this characteristic is still unclear. This study aimed to identify the <em>SUT</em> genes of millet and to assess their expression in drought conditions. Five <em>SUT</em> genes (<em>EcSUT1</em>-<em>EcSUT5</em>) were identified that encode proteins with 9–12 transmembrane domains. Phylogenetic analysis clustered these SUT members across all three main SUT groups, suggesting an evolutionary divergence within the family. Synteny analysis revealed conserved genomic regions, with <em>EcSUT2</em> showing 91–94% identity with orthologs in closely related grasses. Structural models further confirmed their typical transmembrane architecture. Interaction analysis identified EcSUT2 as a key interaction with SWEET transporters. Furthermore, the promoter regions of <em>EcSUT2</em> and <em>EcSUT5</em> were found to be enriched with hormone and stress-responsive elements. Under drought conditions, <em>EcSUT1-EcSUT4</em> displayed transient induction, while <em>EcSUT5</em> showed sustained upregulation, especially in the roots, notably after 48 h. The finger millet SUT family exhibits evolutionary conservation within grasses, with individual genes that play different roles in stress response. The persistent upregulation of <em>EcSUT5</em> under drought strongly suggests its involvement in maintaining sucrose transport during long-term adverse conditions. This candidate gene requires further functional validation to uncover the stress dynamics for sustainable crop improvement.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100592"},"PeriodicalIF":2.8,"publicationDate":"2025-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145332239","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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