Journal of Genetic Engineering and Biotechnology最新文献

{"title":"Gender-specific insights into TTN mutation: potential biomarker for female risk in kidney renal clear cell carcinoma","authors":"Ayan Saha ,&nbsp;Senzuti Sharmin ,&nbsp;Tazin Ahmed ,&nbsp;Sadia Tabassum ,&nbsp;Ayan Roy ,&nbsp;Pallab Kar ,&nbsp;Paromita Biswas ,&nbsp;Jannatul Ferdoush","doi":"10.1016/j.jgeb.2025.100506","DOIUrl":"10.1016/j.jgeb.2025.100506","url":null,"abstract":"<div><div>Kidney Renal Clear Cell Carcinoma (KIRC) is a leading cause of cancer death worldwide, but its early detection remains hindered by a lack of genetic markers. Our study aims to find prospective biomarkers that could serve as prognostic indicators and help in the identification of efficient drug candidates for KIRC treatment. Importantly, this study identifies the hub genes that play a crucial role in KIRC and their impact on male and female patients. The cBioPortal was used to identify frequently mutated genes across seven KIRC studies. Additionally, GSE168845 was employed to identify the differentially expressed genes. The analysis revealed that the titin (TTN) gene was mutated and upregulated in KIRC. Subsequently, differential genes of wild-type TTN versus mutant TTN were identified using TNMplot. The NetworkAnalyst tool was used to conduct KEGG analysis and PPI analysis on these genes. Furthermore, the Kaplan-Meier Plotter was utilized to perform overall survival analysis. Our findings indicated that the TTN gene leads to poorer prognosis in women than in men. We also discovered that the female-specific prolactin signaling pathway plays a significant role in the progression of KIRC. Moreover, our study suggested that the GDF15 gene, involved in the prolactin signaling pathway, has a worse prognosis for KIRC in women than in men. Additionally, mRNA expression analysis showed a negative correlation between GDF15 and MAPK14 in KIRC. Collectively, our research indicates that TTN, GDF15, and MAPK14 can serve as prognostic biomarkers in female KIRC patients, offering prospects for enhanced treatment and patient outcomes in these cancers.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 3","pages":"Article 100506"},"PeriodicalIF":3.5,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144204332","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}

{"title":"In-Silico discovery of novel cephalosporin antibiotic conformers via ligand-based pharmacophore modelling and de novo molecular design","authors":"Rayhan Chowdhury ,&nbsp;Samia Akter Saima ,&nbsp;Md. Al Amin ,&nbsp;Md. Kawsar Habib ,&nbsp;Ramisa Binti Mohiuddin ,&nbsp;Ali Mohamod Wasaf Hasan ,&nbsp;Roksana Khanam ,&nbsp;Shahin Mahmud","doi":"10.1016/j.jgeb.2025.100514","DOIUrl":"10.1016/j.jgeb.2025.100514","url":null,"abstract":"<div><div>Antibiotic resistance poses a significant global challenge as bacteria evolve in response to antibiotic use, leading to prolonged hospitalizations, increased healthcare costs, and higher mortality rates. Cephalosporins, a class of beta-lactam antibiotics, are commonly employed to manage infections; however, their misuse and overuse have contributed to resistance development. In response, in silico methods have emerged as cost-effective and efficient tools for drug discovery. This research aims to predict new compounds using ligand-based pharmacophore models while optimizing existing drugs. We employed a de novo approach to synthesize models of cephalosporin structural motifs, integrating the β-lactam core with potential antibiotic candidates. A shared features pharmacophore (SFP) model was constructed using cephalosporins from PubChem, including cephalothin, ceftriaxone, and cefotaxime. The model comprises hydrogen bond acceptors, hydrogen bond donors, aromatic rings, hydrophobic regions, and negatively ionizable sites. Its robustness was evidenced by a goodness-of-hit (GH) score of 0.739. The generated pharmacophore model, with a score of 0.9268, was utilized to screen a drug library, initially assessing 19 compounds. After the drug-likeness screening, seven promising compounds were identified. These candidates were then fused with the cephalosporin core using genetic algorithms and fragment-based design, resulting in 30 novel synthetic models. Most of these models demonstrated a cephalosporin core, over 70 % average similarity, a TPSA (NO) ≤ 99.85 Å², a drug-likeness (QED) ≥ 0.6, and a Synthetic Accessibility Score (SAScore) ≤ 4.3. Molecular docking and MD simulation evaluations highlighted two candidates—Molecule 23 and Molecule 5, demonstrating superior binding affinities to Penicillin-binding protein 1a (PDB ID: 2V2F) compared to controls. To ensure feasible synthesis, molecular architecture comparison and computational retrosynthesis were performed, confirming the likelihood of successful laboratory synthesis. These findings advance the fight against antimicrobial resistance by establishing a method for designing new, highly effective antibiotic drugs.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 3","pages":"Article 100514"},"PeriodicalIF":3.5,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144196377","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}

{"title":"Bioremediation of crude oil and heavy metal pollutants in marine environment by biosurfactant, rhamnolipid isolated from Stutzerimonas stutzeri − MW15","authors":"J.B. Sony ,&nbsp;W.A. Manjusha ,&nbsp;V.S. Sangeetha ,&nbsp;Salom Gnana Thanga Vincent ,&nbsp;T. Citarasu ,&nbsp;J.R. Anusha","doi":"10.1016/j.jgeb.2025.100507","DOIUrl":"10.1016/j.jgeb.2025.100507","url":null,"abstract":"<div><h3>Objectives</h3><div>The current research aimed to study the biodegradation potential of biosurfactants isolated from marine bacteria against crude oil and heavy metals.</div></div><div><h3>Methods</h3><div>Hemolytic activity, oil displacement, drop collapse, tilted glass slide, and emulsification index tests were employed for screening the biosurfactant production efficiency of marine bacteria which was cultured on an enrichment mineral medium. Based on the highest emulsification activity, the most effective bacterial isolates were selected and subjected to biosurfactant isolation. Further, the characterization using TLC, FTIR, and LC-MS were performed. The bacteria and genes that produced biosurfactants have been identified via 16S rRNA sequence analysis.</div></div><div><h3>Results</h3><div>The isolate MW 15 was selected for structural identification given its maximum oil displacement activity, effective surface tension reduction potential, and favourable emulsification index (E₂₄) of 51.3 %. The purified biosurfactant from MW 15 exhibited structural similarities to rhamnolipid biosurfactant. The biosurfactant-produced strain was identified as <em>Stutzerimonas stutzeri</em> by 16Sr RNA sequencing and the nucleotide sequences were deposited in GenBank with accession number PP779775. Mega 11 software was employed for constructing the phylogenetic tree, and it was confirmed that a gene which produces rhamnolipid (rhlA) was present.</div></div><div><h3>Conclusion</h3><div>Totally eight bacteria were isolated from petroleum hydrocarbon-contaminated marine harbour water. The isolate <em>Stutzerimonas stutzeri</em> showed better production of biosurfactants and biodegradation ability when compared with other biosurfactant-produced isolates. The current investigation promises the use of marine bacteria to produce biosurfactants with biodegradability, less toxicity, and eco-friendly nature.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 3","pages":"Article 100507"},"PeriodicalIF":3.5,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144170358","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}

{"title":"Integrative bioinformatics analysis unveils hub transcription factors and their interacting drugs in immunoglobulin A nephropathy: Implications for pathogenesis and treatments","authors":"YiRui Wang ,&nbsp;Yang Yu ,&nbsp;Rexidan Zaker","doi":"10.1016/j.jgeb.2025.100513","DOIUrl":"10.1016/j.jgeb.2025.100513","url":null,"abstract":"<div><h3>Introduction</h3><div>Several studies identified genetic factors and key cellular signaling associated with developing immunoglobulin A nephropathy (IgAN). However, there is still a lack of understanding regarding the relationship between hub-transcription factors (TFs) encoding genes and changes in immunogenic activity. Our objective was to identify hub-TF encoding genes associated with immune cell infiltrations, immunogenic pathway activity, and potential drug candidates in IgAN through bioinformatics techniques.</div></div><div><h3>Methods</h3><div>We utilized GSE104948, GSE93798, GSE115857, GSE37460, and GSE35487 to identify key significant DEGs and validation in IgAN relative to the control. Next, we employed various bioinformatics approaches to investigate the key genes and their relationship with immunity in IgAN. Finally, we identitified enriched drugs and elcudate their molecular interactions with TFs via molecular docking approaches.</div></div><div><h3>Results</h3><div>We identified 1,123 differentially expressed genes (DEGs) between IgAN and control samples, comprising 342 upregulated genes and 780 downregulated genes. The upregulated genes are linked to immune-related biological processes and KEGG pathways, while the downregulated genes are associated with metabolic processes. Five significant clusters were identified, enriched in several KEGG pathways. We explored 26 hub-TF encoding genes, including <em>GATA2, HDAC1, TSC22D3, SOX9, RARA, RORA, KLF5, KMT2A, FOSB,</em> and <em>FOSL1</em>, which were consistently dysregulated in IgAN patients. Immunogenic analysis revealed increased levels of Th1 cells, pDCs, monocytes, M2 macrophages, fibroblasts, endothelial cells, and activated dendritic cells in IgAN. The activity of various immunological pathways was also elevated. The expression of hub-TFs like <em>GATA2, HDAC1, TSC22D3, SOX9, RARA, RORA, KLF5, KMT2A, FOSB,</em> and <em>FOSL1</em> correlated with immune signatures and pathways in IgAN. Additionally, these hub-TFs were linked to diagnostic efficacy and drug interactions. Molecular docking identified key drug candidates for inhibiting HDAC1 and modulating RARA, suggesting their potential for IgAN treatment.</div></div><div><h3>Conclusions</h3><div>We identified key hub-TFs and their association with immune infiltration and immune pathways linked to IgAN initiation and progression. These findings provide important insights into the immunological mechanisms driving IgAN and propose potential treatment approaches. Molecular docking further revealed key drug candidates for inhibiting and modulating these targets, highlighting their therapeutic potential for IgAN.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 3","pages":"Article 100513"},"PeriodicalIF":3.5,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144169655","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}

{"title":"Beyond the known: Unraveling the existence of novel Trichinella genotypes (T14 and T15) in India and expanding the species complex","authors":"Rasmita Panda ,&nbsp;Anil Kumar Nehra ,&nbsp;Hira Ram ,&nbsp;Mathesh Karikalan ,&nbsp;Priyanka Kumari ,&nbsp;Rajat Garg ,&nbsp;Partha Sarathi Banerjee ,&nbsp;Abhijit Pawde ,&nbsp;Aditi Sharma ,&nbsp;Mukesh Gupta ,&nbsp;Raj Kumar Singh","doi":"10.1016/j.jgeb.2025.100512","DOIUrl":"10.1016/j.jgeb.2025.100512","url":null,"abstract":"<div><div>The <em>Trichinella</em> species complex includes 10 recognized species and three genotypes with global distribution, impacting significant health and economic burdens on livestock, wildlife, and humans. In India, trichinellosis is an under recognized zoonotic disease. Investigating the taxonomic status, genetic diversity and phylogeography of Indian <em>Trichinella</em> isolates is crucial for understanding the disease's regional dynamics. This study used International Commission on Trichinellosis (ICT) recommended multiplex PCR (mPCR) followed by sequencing for identification of the Indian <em>Trichinella</em> isolates up to species level. Multiplex PCR assay yielded band pattern similar to either single infection with <em>T. nelsoni</em> or mixed with <em>T. britovi</em> in leopards and tigers. However, sequencing of mPCR products revealed an increase in base composition. Further molecular characterization was performed using five nuclear genes/regions (<em>18S rRNA</em>, 5S ISR, ESV, ITS1, and ITS2), and three mitochondrial genes (<em>coxI</em>, <em>cytb</em>, and mt-lsr). Phylogenetic analyses (maximum likelihood and Bayesian inference) based on the molecular markers (<em>coxI</em>, 5S ISR, ITS1, and ITS2) highlighted the genetic variation among the Indian isolates, and positioned them as sister clades to <em>T. britovi</em> or <em>T. nelsoni</em> or as an independent taxon. Furthermore, the variable region of ESV also presented a series of unique nucleotides in the Indian isolates which unequivocally differentiated them from known <em>T. nelsoni</em> and <em>T. britovi</em> sequences. Based on the molecular data, six isolates were identified as <em>T. nelsoni</em>-like species, designated as T14 genotype; one isolate with a unique genotype, labelled as genotype T15; and three isolates exhibited mixed infections of <em>T. britovi</em> and the T14 genotype. This study suggests the presence of two novel <em>Trichinella</em> genotypes, T14 and T15, each with distinct genetic profile, emphasizing the role of leopards and tigers as sentinel hosts for <em>Trichinella</em> in India.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 3","pages":"Article 100512"},"PeriodicalIF":3.5,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144134203","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}

{"title":"Reverse vaccinology and immunoinformatics approaches for multi-epitope vaccine design against Klebsiella pneumoniae reveal a novel vaccine target protein","authors":"Mayada M. Elfadil ,&nbsp;Samah Omer A. Samhoon ,&nbsp;Moaaz M. Saadaldin ,&nbsp;Sabah A.E. Ibrahim ,&nbsp;Ahmed Abdelghyoum M. Mohamed ,&nbsp;Omnia H. Suliman ,&nbsp;Osama Mohamed ,&nbsp;Nadzirah Damiri ,&nbsp;Mohd Firdaus-Raih ,&nbsp;Sofia B. Mohamed ,&nbsp;Qurashi. M. Ali","doi":"10.1016/j.jgeb.2025.100510","DOIUrl":"10.1016/j.jgeb.2025.100510","url":null,"abstract":"<div><div><em>Klebsiella pneumoniae</em> (<em>K. pneumoniae</em>), a Gram-negative pathogen, is a leading cause of hospital-acquired infections in Sudan and worldwide. The emergence of multidrug-resistant (MDR) strains has severely limited treatment options, underscoring the urgent need for an effective vaccine. In this study, we employed reverse vaccinology and immunoinformatics to design a novel multi-epitope vaccine targeting the hypervirulent NUBRI-K strain. Two conserved, non-host homologous iron acquisition proteins, IucA/IucC and FyuA, were prioritized as targets. The vaccine construct integrates six B-cell, six cytotoxic T lymphocyte (CTL), and six helper T lymphocyte (HTL) epitopes, linked by optimized spacers and fused to a β-defensin adjuvant. Computational analyses confirmed strong antigenicity (1.0429), non-allergenicity, and favorable solubility (0.477). Molecular docking revealed high-affinity binding to Toll-like receptor 4 (TLR4) (−278.22 kcal/mol), stabilized by eight hydrogen bonds and two salt bridges. Structural validation showed that 91 % of residues were located in favored regions of the Ramachandran plot. Additionally, CABSflex 2.0 dynamics analysis confirmed stable vaccine–TLR4 interactions, with minimal residue-level fluctuations (RMSF &lt;1.5 Å), indicating conformational stability of the complex. In silico immune simulations predicted potent humoral and cellular responses, including elevated IgG/IgM titers, T-cell proliferation, and IFN-γ secretion. The construct was further optimized for mammalian expression, achieving an ideal GC content (48.27 %) and a codon adaptation index (CAI) of 1.0, facilitating efficient in silico cloning into the pcDNA3 vector. By targeting conserved iron acquisition systems, this vaccine candidate presents a promising strategy to combat antibiotic-resistant K. pneumoniae while minimizing selective pressure. Future in vitro and in vivo studies are warranted to validate its immunogenicity and protective efficacy<em>.</em></div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 3","pages":"Article 100510"},"PeriodicalIF":3.5,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144116743","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}

{"title":"Exploring the antibacterial potential of environmental Pseudomonas aeruginosa isolates: Insights from in vitro studies and genome mining approaches","authors":"Md. Saddam Hossain,&nbsp;Afroza Aktar Sharna,&nbsp;Sumaiya Sharmin,&nbsp;Tahrima Arman Tusty,&nbsp;Abu Hashem,&nbsp;Palash Kumar Sarker","doi":"10.1016/j.jgeb.2025.100508","DOIUrl":"10.1016/j.jgeb.2025.100508","url":null,"abstract":"<div><div>Microorganisms are a significant source of antimicrobial agents, accounting for over half of the antibiotics used in healthcare today. This study focused on isolating and screening antibacterial microorganisms from soil samples, followed by a genome-based analysis of the most potent isolates. A total of 231 bacterial isolates were obtained from 63 soil samples collected across Dhaka, Sylhet, and Cox’s Bazar in Bangladesh. Among these, 51 isolates showed antibacterial activity in primary screening using the perpendicular streak method, while 28 exhibited activity in secondary screening via the agar well diffusion method against <em>Escherichia coli</em> ATCC35218, <em>Staphylococcus aureus</em> ATCC6538, <em>Bacillus pumilus</em> ATCC14884, <em>Klebsiella aerogenes</em> ATCC13048, <em>Salmonella typhimurium</em> ATCC13311, <em>Pseudomonas aeruginosa</em> ATCC9027, <em>Micrococcus luteus</em> ATCC10240, <em>B. cereus</em> ATCC10876, <em>Proteus vulgaris</em> ATCC8427, and <em>B. subtilis</em> ATCC6633. All primary screening positive isolates were identified via 16S rRNA analysis, revealing eight genera: <em>Streptomyces</em> (5), <em>Sinomonas</em> (1), <em>Nocardiopsis</em> (3), <em>Arthrobacter</em> (1), <em>Micrococcus</em> (1), <em>Pseudomonas</em> (27), <em>Microbacterium</em> (1) and <em>Bacillus</em> (6). The top five most promising isolates were identified as <em>Pseudomonas aeruginosa</em>, exhibiting strong antagonistic activity, and underwent whole-genome sequencing. Genome mining revealed multiple biosynthetic gene clusters (BGCs), indicating the production of known and unknown antimicrobial compounds, including Pf-5 pyoverdine, Azotobactin D, Pyochelin, and Pyoverdine SMX-1. This study is the first to combine whole-genome analysis with antibacterial activity assessment, highlighting <em>Pseudomonas aeruginosa</em> as a prolific source of bioactive secondary metabolites.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 3","pages":"Article 100508"},"PeriodicalIF":3.5,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144071612","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}

{"title":"Analytical and biological assessment of Magnolia champaca L. stem bark: Integrating ATR-FTIR, GC–MS, thrombolytic activity, brine shrimp lethality and molecular docking","authors":"Md. Mahadi Hasan ,&nbsp;As-Sazzad Mahmud Nishan ,&nbsp;Most. Humayra Binta Rashid ,&nbsp;Bijoy Chandra Ghos ,&nbsp;Jaytirmoy Barmon","doi":"10.1016/j.jgeb.2025.100505","DOIUrl":"10.1016/j.jgeb.2025.100505","url":null,"abstract":"&lt;div&gt;&lt;div&gt;Cancer and cardiovascular disease are two of the most significant health challenges worldwide. These diseases are responsible for morbidity and mortality, leading to a substantial burden on healthcare systems and economic resources. Numerous innovative therapies have been proposed for combating cancer and cardiovascular disease like thrombosis; however, many of these treatments involve synthetic drugs that may have undesirable side effects. Consequently, the current research aimed to explore the medicinal properties of phytochemicals derived from &lt;em&gt;Magnolia champaca&lt;/em&gt; L. This investigation utilized both &lt;em&gt;in vitro&lt;/em&gt; and &lt;em&gt;in silico&lt;/em&gt; approaches. The identification of phytocompounds were employed by using ATR-FTIR and GC–MS. Thrombolytic activity was assayed using human venous blood and cytotoxicity was assessed through lethality test using nauplii of &lt;em&gt;Artemia salina&lt;/em&gt; and finally the molecular docking analysis was performed using a docking software named AutoDock Vina to clearly understand about the interactions of GC–MS identified secondary metabolites with target proteins. The ATR-FTIR spectrum of &lt;em&gt;Magnolia champaca&lt;/em&gt; specifies the presence of some alkaloids, polysaccharides, flavonoids as well as glycosidic phytocompounds and GC–MS data identified 23 compounds from crude methanolic extract and among them 2,4-Di-&lt;em&gt;tert&lt;/em&gt;-butylphenol; 3-Ethyl-3-hydroxyandrostan-17-one; Hexadecanoic acid, methyl ester; Di-n-octyl phthalate were prominent. The &lt;em&gt;in vitro&lt;/em&gt; thrombolytic assay demonstrated that Trans-Syringin and CHF resulted in significant blood clot lysis, achieving 59.39 ± 1.79 % and 45.66 ± 3.63 % respectively comparing 75.75 ± 2.96 % with standard streptokinase. The brine shrimp bioassay indicated moderate to strong toxicological effect. Specifically, Trans-Syringin and the ethyl acetate fraction (EAF) demonstrated considerable cytotoxicity, showing the net values of LC&lt;sub&gt;50&lt;/sub&gt; were 22.39 µg/ml and 61.78 µg/ml, respectively contrary to 11.45 µg/ml of vincristine sulfate (standard). Molecular docking analysis were conducted to explore the synergistic effects of the compounds identified through GC–MS analysis on tissue plasminogen activator and human topoisomerase-II. The compounds 3-Ethyl-3-hydroxyandrostan-17-one; Cadina-1(10),4-diene and 1,1,7-Trimethyl-4-methylenedecahydro-1H-cyclopropa[e]azulen-7-ol-, (1aR-(1a.alpha.,4a.alpha.,7.beta.,7a.beta.,7b.alpha.))- demonstrated high binding affinities of −7.7, −7.3, and −7.1 kcal/mol, respectively, for tissue plasminogen activator where streptokinase (standard) had −6.5 kcal/mol. For human topoisomerase-II, 3-Ethyl-3-hydroxyandrostan-17-one; Caryophyllene-(I1) and Cadina-1(10),4-diene exhibited binding affinities of −8.0, −7.9 as well as −7.8 kcal/mol correspondingly, while standard vincristine had −8.1 kcal/mol. These findings suggest that &lt;em&gt;Magnolia champaca&lt;/em&gt; contains active phytochemicals with significant potentials for diverse pharmacologi","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100505"},"PeriodicalIF":3.5,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143937359","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}

{"title":"Genome-wide association study −Driven drug repositioning for the treatment of insomnia","authors":"Rahmat Dani Satria ,&nbsp;Wirawan Adikusuma ,&nbsp;Usi Sukorini ,&nbsp;Devy Eka Avitasari ,&nbsp;Indra Sari Kusuma Harahap ,&nbsp;Mohammad Hendra Setia Lesmana ,&nbsp;Lalu Muhammad Irham ,&nbsp;Nur Imma Fatimah Harahap ,&nbsp;Pranindya Rinastiti ,&nbsp;Donytra Arby Wardhana ,&nbsp;Richardus Wisnandito Prabasaktya ,&nbsp;Chiou-Feng Lin ,&nbsp;Aprilia Paramitasari ,&nbsp;Andrian Fajar Kusumadewi","doi":"10.1016/j.jgeb.2025.100502","DOIUrl":"10.1016/j.jgeb.2025.100502","url":null,"abstract":"<div><div>Insomnia is a prevalent sleep disorder characterized by difficulty initiating or maintaining sleep, leading to severe health complications, increased mortality, and substantial socioeconomic burdens. Despite therapeutic advancements, effective pharmacological interventions remain limited, necessitating alternative approaches for drug discovery. This study aimed to identify potential therapeutic targets for insomnia by integrating gene network analysis, genomic data, and bioinformatics-driven drug repurposing strategies, aligning with the United Nations’ Sustainable Development Goal (SDG) 3: Good Health and Well-being. Insomnia-associated Single Nucleotide Polymorphisms (SNPs) were retrieved from the GWAS catalog, yielding 3,952 loci. Insomnia risk genes were identified by linking these loci to proximal SNPs (r² ≥ 0.8) in Asian populations using HaploReg v4.2, resulting in 1,765 candidate genes. A bioinformatics pipeline incorporating ten functional annotations and drug-gene interaction was employed to prioritize gene targets and identify novel repurposed drugs with potential biological relevance to insomnia. Drug-Gene Interaction Database (DGIdb) analysis identified seven druggable targets among 27 biologically significant insomnia risk genes, corresponding to 12 existing drugs. Notably, <em>NRXN1</em> emerged as a highly promising target due to its strong functional annotation score and its known interaction with Duloxetine hydrochloride and nicotine polacrilex. This study underscores the potential of bioinformatics-driven gene network analysis in identifying drug repurposing candidates for insomnia. Further experimental validation is warranted to elucidate the therapeutic mechanisms of NRXN1 modulation in insomnia treatment.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100502"},"PeriodicalIF":3.5,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143937360","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}

{"title":"Transcriptome Derived Artificial neural networks predict PRRC2A as a potent biomarker for epilepsy","authors":"Wayez Naqvi,&nbsp;Prekshi Garg,&nbsp;Prachi Srivastava","doi":"10.1016/j.jgeb.2025.100503","DOIUrl":"10.1016/j.jgeb.2025.100503","url":null,"abstract":"<div><div>Epilepsy refers to the occurrence of two or more than two reiterative seizures. The occurrence of seizure is governed by the excessive electrical discharges in the cortex of the brain. Bioinformatics is crucial in diagnosing, prognosticating, and treating neurological disorders. It uses methodologies, computational tools, software, and databases to probe disease molecular underpinnings and identify biomarkers. It aids clinicians in addressing patient parameters and translational research. Artificial neural networks (ANNs) are computer models that attempt to mimic the neurons present in the human brain. This computerized neuronal model is used for analyzing and comprehending large and complex data sets. In the present study, three GEO datasets (GSE190451, GSE140393, and GSE134697) were retrieved from NCBI for the identification of differentially expressed genes using the DESeq2 package. The study identified 7 up-regulated genes (PRRC2A, FCGR3B, HLA-DRB, ENSG00000280614, ENSG00000281181, SLN, C4A) in patients with epilepsy. Furthermore, WEKA software was used for feature selection and classification of DEGs using feature selection algorithms namely Correlation Feature Selection, ReliefF, and Information Gain and classification methods such as Logistic regression, Classification via regression, Random forest, Random subspace, and Logistic model trees. After the analysis, out of the 7 genes, the C4A gene was removed as it yielded the lowest feature selection statistics. Lastly, R Studio was used for constructing the Artificial Neural Network of the 6 identified DEGs. The model’s performance was evaluated using the “pROC” R package, and an AUC of 0.720 was obtained, indicating that the model had excellent classification accuracy. The NeuralNet package of R revealed that PRRC2A had the highest generalized weight value indicating the increased expression of these genes when all other parameters are constant. Therefore, PRRC2A can be used as a potential biomarker for the diagnosis of epilepsy.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100503"},"PeriodicalIF":3.5,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143937358","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}