Journal of Genetic Engineering and Biotechnology最新文献

{"title":"Analysis of the current status of genetic diversity in Liaoning Huoyan goose based on microsatellite markers","authors":"Qianhui Wang ,&nbsp;Jiaming Wang ,&nbsp;Yan Zheng ,&nbsp;Changjiang Li ,&nbsp;Xingtang Dou ,&nbsp;Zhongzan Cao ,&nbsp;Yue Gao ,&nbsp;Bing Xue ,&nbsp;Di Han ,&nbsp;Xinhong Luan","doi":"10.1016/j.jgeb.2025.100517","DOIUrl":"10.1016/j.jgeb.2025.100517","url":null,"abstract":"<div><div>In this study, microsatellite loci in geese were initially screened, after which a multiplex PCR system was constructed and the genetic diversity and genetic structure of 40 samples from each of the three Huoyan goose populations in Liaoning were analyzed using the STR typing test. The results showed that 12 microsatellite loci were screened, and one quadruple PCR system, two triple PCR systems and one double PCR system were constructed with consistent and reliable reproducibility. A total of 90 alleles were detected in 120 samples, the number of alleles(Na), observed heterozygosity (Ho), expected heterozygosity (He) and polymorphic information content(PIC) of the three populations ranged from 5.083 to 6.083, from 0.149 to 0.184, from 0.555 to 0.577 and from 0.503 to 0.512.respectively, the populations present an unbalanced state, and the genetic diversity of three populations was highly polymorphic and highly inbred. The results of Principal Coordinates Analysis (PCoA) and genetic structure analysis showed that the genetic backgrounds of the three populations of Huoyan geese were similar, with close affinities and frequent gene exchanges.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 3","pages":"Article 100517"},"PeriodicalIF":3.5,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144279878","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":"Gut microbiome composition and diversity of wild-caught and hatchery-bred milkfish (Chanos chanos) fry","authors":"Gardel Xyza L. Silvederio ,&nbsp;Therese F. Javellana ,&nbsp;Ande Bryle N. Genciana ,&nbsp;Maria Alexandra G. Fontanilla ,&nbsp;Rex Ferdinand M. Traifalgar ,&nbsp;Fredson H. Huervana ,&nbsp;Carmelo S. del Castillo","doi":"10.1016/j.jgeb.2025.100520","DOIUrl":"10.1016/j.jgeb.2025.100520","url":null,"abstract":"<div><div>Milkfish is the most produced finfish in the Philippines, with approximately 75 % of its fry sourced from hatcheries. Despite numerous studies on gut microbiota of wild and cultured fish species, the diversity and functional roles of the milkfish fry gut microbiome remain poorly understood. This study presents the first gut microbiome profiles of wild and hatchery-bred milkfish fry using 16S rRNA amplicon analysis. A total of 437 OTUs were recovered and significant differences in gut bacterial communities among fry from different sources was observed, indicating that habitat is a key determinant of gut microbiome diversity. The core gut microbiota analysis identified <em>Vibrionaceae</em> and <em>Roseobacteraceae</em> as the most common and abundant bacterial families across fry sources. However, <em>Paenibacillaceae</em> and <em>Bacillaceae</em> under Phylum Bacillota were dominant in wild fry sources, particularly Hamtic and Kirayan, whereas families belonging to Phyla Cyanobacteriota, and Thermodesulfobacteria were more prevalent in Dumagas and Kirayan hatchery fry sources. Functional predictions of the gut bacterial microbiome revealed 26 differentially abundant pathways between wild-caught and hatchery-bred fry, including those related to metabolism, organismal systems, cellular processes, environmental and genetic information processing. These findings highlight significant variations in gut microbiome composition, diversity, and functional potential across different sources of wild-caught and hatchery-bred fry. Understanding these source-specific microbial communities could provide insight into the development of interventions that can improve gut health and enhance milkfish hatchery practices. It can also generate information on ideal fry selection across local milkfish sources that will enhance larval productivity and survival in the succeeding nursery and grow-out culture stages.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 3","pages":"Article 100520"},"PeriodicalIF":3.5,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144262379","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":"scp3 gene expression during ovarian differentiation in Hypoatherina tsurugae (Pisces; Atheriniformes)","authors":"Dilip Kumar Bej ,&nbsp;Sullip Kumar Majhi","doi":"10.1016/j.jgeb.2025.100518","DOIUrl":"10.1016/j.jgeb.2025.100518","url":null,"abstract":"<div><div>The <em>scp3</em> gene encodes the SYP3 protein, which forms the synaptonemal complex required for pairing homologous chromosomes throughout the prophase of the first meiosis. In addition, it plays a significant role in the formation of germ cells. The 978 bp <em>scp3</em> mRNA transcript from <em>Hypoatherina tsurugae</em> was cloned and sequenced. The gene comprises an open reading frame (ORF) of 720 bp encoding 240 amino acids (AA), which are identical to those of various other fish species. A phylogenetic tree was created by comparing the mRNA sequences of 50 fish species from the taxa accessible in the NCBI database, utilizing <em>Acipenser ruthenus</em> as an out-group. The tree revealed a higher homology of <em>scp3</em> from <em>H. tsurugae</em> with <em>Maelanotaenia boesemani</em>, the 2 forming a single clade. Using qRT-PCR, <em>scp3</em> mRNA transcript expression was investigated and found to be highly expressed in <em>amhy-</em> (females) during the early gonadal differentiation phase, from day 0 to week 10 after hatching. In contrast, <em>amhy+</em> (males) showed comparatively low expression. The differentiation of male and female gonads was determined six weeks after hatching, based on histological analysis of gonads recovered from biweekly collected larvae throughout the sex determination/differentiation stage. In this phase, primary oocytes are predictable. The data obtained in this study provide crucial information for further understanding the molecular mechanisms involved in sex differentiation and determination in fish.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 3","pages":"Article 100518"},"PeriodicalIF":3.5,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144262468","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":"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}