Journal of Genetic Engineering and Biotechnology最新文献

{"title":"Profiling of proteases involved in SARS-CoV-2 pathogenesis in human saliva: Influence of age and gender","authors":"Mentalla Motaz Abdellatif ,&nbsp;Azza El Amir ,&nbsp;Said Shalaby ,&nbsp;Michael Kirschfink ,&nbsp;Rola Nadeem ,&nbsp;Dina Nadeem Abd-Elshafy ,&nbsp;Mahmoud Mohamed Bahgat","doi":"10.1016/j.jgeb.2025.100509","DOIUrl":"10.1016/j.jgeb.2025.100509","url":null,"abstract":"<div><h3>Background</h3><div>SARS-CoV-2 enters human cells via angiotensin-converting enzyme 2 (ACE2). In silico experiments also demonstrated possible SARS-CoV-2 binding to dipeptidyl peptidase 4 (DPP-4) during cell entry. Moreover, matrix metalloproteinase 2 (MMP-2) is involved in the SARS-CoV-2 cell fusion process.</div></div><div><h3>Aims</h3><div>To study expression and activity profiles of implicated enzymes in SARS-CoV-2 infection in various age groups of both genders and discuss the possible impact of this on COVID-19 outcome.</div></div><div><h3>Methods</h3><div>Saliva from different age groups was used to profile MMP-2 and gelatinase enzymes by zymography. Enzyme activities resulting from the cleavage of the H-Arg-Pro-pNA substrate were measured using a microplate reader. ACE2 transcription and translation were quantified using qRT-PCR and ELISA. Statistical analysis was used to identify the presence of significant differences.</div></div><div><h3>Results</h3><div>Zymography demonstrated different gelatinase activities in a range of ∼180–30 kDa and showed distinct bands at ∼96, 72, 66, 60, and 40 kDa. Comparing MMP-2, DPP-4, DPP-4/ACE2 activities, ACE2 protein, and mRNA levels between genders showed p-values of 0.0142, 0.1056, 0.1859, 0.6411, and 0.4797, whereas correlations with age showed correlation coefficient (r) values of 0.1377, 0.4185, 0.0597, −0.0993, and −0.0073, respectively. The r values between ACE2 protein and ACE2 mRNA with DPP-4 activity were −0.0668 and 0.1935, respectively. The values between both DPP-4 activity and ACE2 protein with MMP-2 activity were −0.0506 and 0.0898, respectively. Results reflected (1) MMP-2 activity is higher among males. (2) DPP-4 activity positively correlates with age. (3) Gender differences in DPP-4 activity, ACE2 protein, and mRNA levels were not statistically significant. (4) Age differences in MMP-2 activity, ACE2 expression were not significant. (5) Inter-enzyme correlations were not observed.</div></div><div><h3>Conclusions</h3><div>The differential activity of both MMP-2 and DPP-4 highlights their potential as risk factors for susceptibility to SARS-CoV-2 infection and COVID-19 severity in males and older groups.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 3","pages":"Article 100509"},"PeriodicalIF":3.5,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144307878","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":"Alternative therapeutic approaches for combating multi-drug-resistant bacteria: Reverse vaccinology against Enterobacter cloacae","authors":"Gabriela Guerrera Soares ,&nbsp;Marcelo Silva Folhas Damas ,&nbsp;Pedro Mendes Laprega ,&nbsp;Rebecca Elizabeth Shilling ,&nbsp;Eduarda Oliva Ribeiro Rangel ,&nbsp;Louise Teixeira Cerdeira ,&nbsp;Murillo Rodrigo Petrucelli Homem ,&nbsp;André Pitondo-Silva ,&nbsp;Andrea Soares da Costa-Fuentes ,&nbsp;Maria-Cristina da Silva Pranchevicius","doi":"10.1016/j.jgeb.2025.100519","DOIUrl":"10.1016/j.jgeb.2025.100519","url":null,"abstract":"<div><div><em>Enterobacter cloacae</em> is a clinically significant opportunistic and multidrug-resistant bacterium that causes a range of hospital-acquired infections, particularly in intensive care units. However, studies on vaccine development have been limited, and no vaccine currently protects against <em>E. cloacae</em>. Here, we employed subtractive proteomics, reverse vaccinology, and immunoinformatic approaches to design a multi-epitope-based vaccine targeting <em>E. cloacae</em>. Analysis of 21 complete <em>E. cloacae</em> genomes associated with human infections revealed 1,352 proteins linked to essentiality, resistance, and/or virulence, 39 of which were non-human and non-gut homologs. From this refined selection, 9 were found to be antigenic, extracellular, or exported to the outer membrane and used to construct 4 multi-epitope vaccines (VEC1-4) containing antigenic (threshold of ≥0.5), non-allergenic, conserved, hydrophilic (GRAVY &lt; 0), exposed, and non-toxic epitopes. They were all processed and presented through the MHC class pathway, while also showing high population coverage. VEC1 showed the most consistent performance, with the highest average binding affinity (−24.07 kcal/mol), docking score (−322.21), and the most favorable dissociation constant at 37 °C. VEC1 was shown to be conformationally stable, with a secondary structure predominantly made up of alpha-helices and coils. The <em>in silico</em> analysis suggested that VEC1 can be efficiently expressed in an <em>E. coli</em> system, and it is currently awaiting <em>in vivo</em> testing to confirm its precise efficacy, safety, and immunogenicity. These findings provide valuable insights for developing novel approaches to prevent and control the spread of multidrug-resistant bacteria.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 3","pages":"Article 100519"},"PeriodicalIF":3.5,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144297583","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":"Multiscale comparative pathogenomic analysis of Vibrio anguillarum linking serotype diversity, genomic plasticity and pathogenicity","authors":"Khandker Shahed ,&nbsp;Ashim Chakma ,&nbsp;Omar Hamza Bin Manjur ,&nbsp;Sk Injamamul Islam","doi":"10.1016/j.jgeb.2025.100522","DOIUrl":"10.1016/j.jgeb.2025.100522","url":null,"abstract":"<div><div><em>Vibrio anguillarum</em> is a major marine fish pathogen causing high mortality and potential zoonotic risks. Understanding its genomic diversity, virulence factors, and antibiotic resistance is crucial for aquaculture disease management. In this study, a comparative pan-genomic analysis of 16 <em>V. anguillarum</em> strains was conducted to examine core and accessory genome diversity, virulence factors, and antibiotic resistance mechanisms. The phylogenetic analysis was conducted using six core genes and SNPs to evaluate evolutionary relationships and pathogenic traits. The core genome contained 2,038 unique ORFs, while the accessory genome had 5,197 cloud genes, confirming an open pangenome. This study identified 118 pathogenic genomic islands, antibiotic resistance genes (tetracycline, quinolone, and carbapenem), and virulence factors, including type VI secretion system (T6SS) components and RTX toxins (hcp-2, vipB/mglB, rtxC). Core genes such as ftsI uncovered substantial evolutionary divergence among species, identifying more than 150 distinct SNPs. Phylogenetic analysis showed serotype-specific clustering, with O1 strains displaying genetic homogeneity, whereas O2 and O3 exhibited divergence, suggesting distinct evolutionary adaptations influencing pathogenicity and ecological interactions. These findings provide primary insights for developing molecular markers and targeted treatments for aquaculture pathogens.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 3","pages":"Article 100522"},"PeriodicalIF":3.5,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144297584","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":"Whole-genome sequencing and biofilm gene characterization in multidrug-Resistant Staphylococcus aureus clinical strains","authors":"Emira Noumi ,&nbsp;Tarek Zmantar ,&nbsp;Nouha Bouali ,&nbsp;Abdulrahman S. Bazaid ,&nbsp;Khulood Fahad Alabbosh ,&nbsp;Kamel Chaieb ,&nbsp;Hisham N. Altayb ,&nbsp;Vincenzo De Feo ,&nbsp;Mejdi Snoussi","doi":"10.1016/j.jgeb.2025.100521","DOIUrl":"10.1016/j.jgeb.2025.100521","url":null,"abstract":"<div><div><em>Staphylococcus aureus</em> is known as a significant contributor to a variety of severe, life-threatening illnesses. Infectious diseases associated with biofilm-producing <em>S. aureus</em> can lead to a substantial increase in morbidity and mortality rates<em>.</em> This study aimed to characterize the whole genomes of eight clinically multidrug-resistant <em>S. aureus</em> strains isolated from several types of human infections sites from Hail Hospital, Saudi Arabia. Biofilm production was evaluated using Congo-red agar plates (CRA), polystyrene microtiter plate technique (MtP), and adherence to human epithelial cells (Hep 2). Additionally, adhesion to abiotic surface (Polyethylene, glass, stainless steel) was assessed using scanning electron microscopy (SEM). Then whole genome sequencing was conducted for all strains to analyze the virulome, resistome and phylogenome using different bioinformatic tools.</div><div>Our results revealed that all <em>S. aureus</em> strains were slime producer on CRA plates with pigmented colonies (black and nearly black morphotypes) and were also able to form biofilm on the surface of several materials with different degrees. All tested strains adhere to Hep2 cell lines with a percentage of infected cells ranging from 45.0 % ± 0.078 to 92.0 % ± 0.022, and a total number of <em>S. aureus</em>/100 cells varying from 5.11 ± 2.14 (Strain S22) to 20.25 ± 5.15 (Strain S14). These results were correlated with those obtained from genome annotation highlighting that all multidrug resistant and biofilm-producing <em>S. aureus</em> strains harbored four <em>ica</em> genes (<em>icaA, icaB, icaC, icaD</em>) and their regulator <em>icaR</em>), clumping factor A and B (<em>clf</em>A and <em>clf</em>B genes), fibronectin binding proteins (fnbA in all strains and fnbB in 87.5 % of tested strains), elastin binding protein (<em>ebps</em> gene), extracellular adherence protein (Eap), staphylococcal protein A (<em>spa</em> gene), and Ser-Asp rich fibrinogen-binding proteins (<em>sdrC</em>). Most of the studied strains contained six to ten genomic islands associated with virulence factors, phage proteins, transcriptional regulators, insertion sequences and antimicrobial resistance genes. The study reported the presence of key adhesion-related genes underscores the colonization potential and pathogenicity in our strains. Additionally, the identification of multiple genomic islands associated with virulence and antimicrobial resistance highlights the need for vigilant monitoring in clinical settings.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 3","pages":"Article 100521"},"PeriodicalIF":3.5,"publicationDate":"2025-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144291174","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":"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}