Journal of Genetic Engineering and Biotechnology最新文献

{"title":"Identification of key biomarker genes in liver hepatocellular carcinoma and kidney renal clear cell carcinoma progression: A shared high-throughput screening and molecular docking method with potentials for targeted therapeutic interventions","authors":"Maisha Tasneem ,&nbsp;Shipan Das Gupta ,&nbsp;Md Jubair Ahmed Jony ,&nbsp;Maya Minkara ,&nbsp;Rajib Kumar Dey ,&nbsp;Jannatul Ferdoush","doi":"10.1016/j.jgeb.2025.100497","DOIUrl":"10.1016/j.jgeb.2025.100497","url":null,"abstract":"<div><h3>Background and objectives</h3><div>Liver Hepatocellular Carcinoma (LIHC) and Kidney Renal Clear Cell Carcinoma (KIRC) are leading causes of cancer death worldwide, but their early detections remain hindered by a lack of genetic markers. Our study aims to find prospective biomarkers that could serve as prognostic indicators for efficient drug candidates for KIRC and LIHC treatment.</div></div><div><h3>Methods</h3><div>To detect differentially expressed genes (DEGs), four datasets were used: GSE66271 and GSE213324 for KIRC, and GSE135631 and GSE202853 for LIHC. Visualization of DEGs was done using heatmaps, volcano plots, and Venn diagrams. Hub genes were identified via PPI analysis and the cytoHubba plugin in Cytoscape. Their expression was evaluated using box plots, stage plots, and survival plots for prognostic assessment via GEPIA2. Molecular docking with PyRx’s AutoDock Vina identified optimal binding interactions between compounds and proteins. Pharmacokinetic and toxicity analyses reinforced the drug-likeness and safety of these compounds.</div></div><div><h3>Results</h3><div>In this study, 47 DEGs were identified, with the top 10 hub genes being <em>TOP2A</em>, <em>BUB1</em>, <em>PTTG1</em>, <em>CCNB2</em>, <em>NUSAP1</em>, <em>KIF20A</em>, <em>BIRC5</em>, <em>RRM2, NDC80</em> and <em>CDC45</em>, chosen for their high MCC scores. Data mining revealed a correlation between TOP2A expression and clinical survival outcomes in KIRC and LIHC patients. Docking studies of the TOP2A structure identified a promising compound from <em>Andrographis paniculata</em> with high binding energy and interactions with TOP2A. Pharmacokinetic and toxicity assessments support its potential as a drug candidate.</div></div><div><h3>Conclusion</h3><div>Our study emphasizes <em>TOP2A</em>’s prognostic significance in KIRC and LIHC and recognizes <em>Andrographis paniculata</em> compound as potential therapeutics, offering prospective for enhanced treatment and patient outcomes in these cancers.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100497"},"PeriodicalIF":3.5,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143859130","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":"Cardioprotective function of mixed spices against myocardial infarction injury: In-vivo and in-silico study","authors":"Md. Abdullah-Al-Mamun ,&nbsp;Dipa Islam ,&nbsp;Dipankar Chandra Roy ,&nbsp;Ayesha Ashraf ,&nbsp;Saifullah ,&nbsp;Chadni Lyzu ,&nbsp;Md. Enamul Kabir Talukder ,&nbsp;Samina Akhter ,&nbsp;Evana Parvin Lipy ,&nbsp;Liton Chandra Mohanta","doi":"10.1016/j.jgeb.2025.100492","DOIUrl":"10.1016/j.jgeb.2025.100492","url":null,"abstract":"<div><div>Myocardial infarction is the permanent necrosis of heart tissue caused by an artery obstruction. It causes an inadequate delivery of oxygen and nutrients, resulting in muscle injury in the afflicted areas. Here, water extract of mixed spices—onion, garlic, ginger, red chili, turmeric, cumin seed, coriander, cardamom, black pepper, cloves, fenugreek, nigella, cinnamon, and carom seed—was prepared to evaluate cardioprotective function in albino rats. To systematically investigate cardioprotective efficacy, isoproterenol was injected into albino rats to induce myocardial injury. The prepared extract was administrated orally to rats daily for 28 days (200 mg/kg body weight) before infusion of isoproterenol (100 mg/kg body weight) on 29th and 30th days. The induced cardiac injury was significantly ameliorated in rats based on cardiac hypertrophy, histopathology, and <em>Caspase-3</em> mRNA expression analysis by qRT-PCR. The Indian Medicinal Plants, Phytochemistry And Therapeutics (IMPPAT) chemical database of 820 natural compounds from the mixed spices was then screened against CASP-3 protein using cheminformatics tools, where thymohydroquinone, 4-isopropylbenzoic acid, and 1-naphthylacetic acid were found to be the best interacting ligands, with binding energy scores of −6.112 kcal/mol, −6.206 kcal/mol, and −6.112 kcal/mol, respectively. Notably, thymohydroquinone exhibited the lowest predicted cytotoxicity. Furthermore, molecular dynamic simulation was used to validate the binding stability of the thymohydroquinone with CASP-3 protein compared to CID-6167 (control). Thus, this study explored that mixed spices have cardioprotective effects in rats and identified thymohydroquinone as a natural lead compound against CASP-3, which may pave the way for the development of pharmacotherapy for myocardial damage.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100492"},"PeriodicalIF":3.5,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143848147","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":"Comparative proteomics and structure-based approach to unravel the therapeutic drug target of Theileria species","authors":"Anusha Majumder ,&nbsp;Jyotisha ,&nbsp;Fouzia Nasim,&nbsp;Insaf Ahmed Qureshi","doi":"10.1016/j.jgeb.2025.100488","DOIUrl":"10.1016/j.jgeb.2025.100488","url":null,"abstract":"<div><div>Theileriosis, caused by protozoan parasites of genus <em>Theileria</em>, primarily affects both domestic and wild ruminants. It can lead to significant economic losses in livestock farming due to decreased productivity and high mortality rates in susceptible animals, while treatment measures are not cost-effective. Since most of mechanisms of this disease remain unknown, this study investigates the differences in the mode of pathogenesis between transforming and non-transforming groups through an <em>in silico</em> comparative proteomics approach to recognize the key players involved in host cell transformation. Although the major biological processes and molecular functions are almost conserved between the two groups, PEST-motif containing secretory proteins of <em>Sfi</em>I, SVSP, and Tash-AT gene families were identified as important candidates with the potential to transform infected host cells. Several members of PEST-motif containing proteins possess signal peptides, nuclear localization signals, and <em>trans</em>-membrane helices, further supporting their potential to transform host cells. Additionally, structural analysis helped in the identification of a parasitic protein (<em>Sfi</em>Ip) from <em>Sfi</em>I family as a plausible drug target. Virtual screening revealed FDA-approved drugs (i.e. atogepant and rimegepant) as promising compounds, showing the highest affinity for <em>Sfi</em>Ip during molecular docking. Further studies, including molecular dynamics simulation, principal component analysis, and free energy landscape, suggested that these drug molecules exhibit the stable interaction with protein. Therefore, our research could facilitate the identification and targeting of novel drug candidates that may be further implemented to recognize effective therapeutics against <em>Theileria</em> infections.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100488"},"PeriodicalIF":3.5,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143806977","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 analysis of endophytic strain PM1 reveals promising plant Growth-Promoting mechanisms in pomegranate","authors":"Poonam Patel,&nbsp;Fenil Patel,&nbsp;Chaitanya Joshi,&nbsp;Madhvi Joshi","doi":"10.1016/j.jgeb.2025.100486","DOIUrl":"10.1016/j.jgeb.2025.100486","url":null,"abstract":"<div><div>The plant ecosystem harbours diverse symbiotic microorganisms with plant growth promoting and biocontrol activities. The gram- negative endophytic bacterium PM1 strain, isolated from the nodal region of pomegranate. The strain PM1 was studied through whole-genome sequencing, functional annotation, and plant growth-promoting trait (PGPT) gene analysis. Phylogenetic tree analysis and 16S rDNA sequencing confirmed its classification within the genus <em>Brucella</em>. The assembled genome size was 5,200,895 bp with a G + C content of 56.4 %. The average nucleotide identity (ANI) analysis revealed a 97.62 % similarity between PM1 and <em>B. anthropi</em> ATCC 49188 T, a type strain derived from human clinical samples, indicating a close relationship with <em>Brucella anthropi.</em> The functional annotation revealed 2,945 PGPT-related genes, including 32 % linked to direct effects (phytohormone signal production, biofertilization, and bioremediation processes) and 67 % to indirect effects (plant colonization, biocontrol, and competitive exclusion). KEGG analysis revealed genes involved in nitrogen metabolism, phosphate solubilization, siderophore production, hormone biosynthesis (gibberellin, cytokinin, and auxin), root colonization, and stress mitigation. Virulence factor database (VFDB) data revealed the absence of complete virulence gene assemblies, indicating limited pathogenic potential. Furthermore, secondary metabolite analysis predicted the potential production of ochrobactin compounds, which are potent siderophores that are important traits associated with PGPTs. The complete genome analysis of <em>Brucella</em> sp. PM1 provides new insights into plant-bacteria interactions, laying a foundation for advanced postgenomic studies and facilitating the development of bioeffective strategies such as biofertilizers or biocontrol agents for sustainable improvement in crop yields.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100486"},"PeriodicalIF":3.5,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143777095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Small interfering RNA: From designing to therapeutic in cancer","authors":"Jyoti Singh ,&nbsp;Abdulaziz S. Saeedan ,&nbsp;Gaurav Kaithwas ,&nbsp;Mohd Nazam Ansari","doi":"10.1016/j.jgeb.2025.100484","DOIUrl":"10.1016/j.jgeb.2025.100484","url":null,"abstract":"<div><div>Cancer has become a significant public health concern worldwide. It is a group of diseases, often resulting from the dysregulation of multiple cellular pathways involved in differentiation, cell proliferation, cell cycle regulation, and DNA repair. These disruptions are primarily caused by genetic mutation and epigenetic alterations which lead to uncontrolled growth and tumor formation. Targeted therapy is a precise and effective strategy to overcome the shortcomings of conventional therapy. RNA interference (RNAi) is a gene-silencing mechanism that has an uncanny ability to target disease-associated genes. Small interfering RNA (siRNA) is a key component of RNAi and has shown promise in silencing oncogenes and inhibiting cancer progression. However, the therapeutic application of siRNA faces several challenges such as poor cellular uptake, short half-life, endosomal escape, immune system activation, and off-target. Strategies to address these challenges are optimized designing of siRNA, advanced delivery systems, and chemical modification to improve cellular uptake and protect from degradation. This review focuses on the therapeutic potential of siRNA in cancer treatment and discusses the action mechanism of siRNA, barriers in siRNA, and strategies to overcome them. The review shed light on the current clinical trial of siRNA-based cancer therapy, along with outcomes and limitations.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100484"},"PeriodicalIF":3.5,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143759705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In silico drug repurposing for potential HPV-induced skin wart treatment − A comparative transcriptome analysis","authors":"Navid Kashani ,&nbsp;Amir Sabbaghian ,&nbsp;Khadijeh Ahmadi ,&nbsp;Mahdi Aalikhani","doi":"10.1016/j.jgeb.2025.100485","DOIUrl":"10.1016/j.jgeb.2025.100485","url":null,"abstract":"<div><h3>Introduction</h3><div>Warts are dermal disorders resulting from HPV infection and can be transmitted by direct contact. Existing treatment approaches, such as topical treatment with salicylate, have low efficiency and demonstrate side effects. Thus, the discovery of potent drug treatments for skin warts is necessary. Here we propose the use of alternative medications for the possible treatment of skin warts with the help of comparative transcriptome analysis and drug repurposing approaches.</div></div><div><h3>Methods</h3><div>Gene expression datasets related to HPV-induced warts and cervical cancer were extracted from the GEO database. Differentially expressed genes (DEGs) were identified using DESeq2 in the Galaxy database. Upregulated DEGs were assessed for druggability using the DGIdb tool. Gene ontology and enrichment analysis were performed to investigate the characteristics of druggable DEGs. A molecular docking virtual screening was conducted using PyRx software to identify potential therapeutic targets for skin warts. The interactions between selected drug candidates and the target protein were analyzed using the BIOVIA Discovery Studio. The physicochemical characteristics of potential pharmaceuticals were evaluated using the SwissADME database. Finally, the molecular dynamics (MD) simulation was performed to validate the stability and dynamic behavior of drug-protein interactions.</div></div><div><h3>Results</h3><div>Based on the findings from gene expression profiling, Integrin Alpha-X (ITGAX, CD11c) has been identified as a candidate protein that is significantly upregulated in individuals afflicted with skin warts. Integrin Alpha-X plays a crucial role in mediating intercellular interactions during inflammatory processes and notably enhances the adhesion and chemotactic activity of monocytes. Through molecular docking, MD, and physicochemical analyses, it has been demonstrated that dihydroergotamine effectively inhibits the ITGAX protein, suggesting its potential as a therapeutic agent for the management of skin warts.</div></div><div><h3>Conclusion</h3><div>Dihydroergotamine can be repurposed as a potential drug in the treatment of skin warts by targeting Integrin Alpha-X protein.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100485"},"PeriodicalIF":3.5,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143735084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular characterization of chromium tolerant and gelatin hydrolyzing bacterial isolates from tannery wastes: Perspective on chrome-tanned leather waste biodegradation in Bangladesh","authors":"Shashanka Shekhar Sarker ,&nbsp;Md.Murshed Hasan Sarkar ,&nbsp;Shamima Akhter Sharmin ,&nbsp;Nourin Tarannum ,&nbsp;Taslima Akter ,&nbsp;Md.Ashraful Alam ,&nbsp;Md.Ibrahim Miah ,&nbsp;Md.Aftab Ali Shaikh ,&nbsp;Sahana Parveen","doi":"10.1016/j.jgeb.2025.100479","DOIUrl":"10.1016/j.jgeb.2025.100479","url":null,"abstract":"<div><div>Improper management of chrome-tanned leather waste (CTLW) might potentially cause adverse environmental consequences. To mitigate that harmful impact, this study aims to find and conduct molecular characterization of bacteria from tannery wastes that can tolerate chromium (Cr) and hydrolyze gelatin. Bacteria from tannery wastes are naturally adapted to Cr; eight Cr(III) tolerant bacteria, namely bacterial isolate (BI) 1 to 8, were isolated from the collected waste samples. The isolated bacteria showed the maximum tolerance concentration (MTC) range of 700 to 1500 ppm for Cr(III) and 200 to 600 ppm for Cr(VI). Physiological and biochemical analysis, including the gelatin hydrolysis activity, identified those isolates up to the genus level. Among the isolates, BI 4, 5, and 7 were able to hydrolyze gelatin. Therefore, 16S rRNA molecular characterization was conducted for those isolates, which confirmed BI 4, 5, and 7 as <em>Bacillus wiedmannii</em> (Accession No: OR564007), <em>Enterococcus faecium</em> (Accession No: OR564008), and <em>Bacillus cereus</em> (Accession No: OR564009), respectively. Bacteria with gelatin hydrolyzing activity can be the potential for degrading hydrothermally treated CTLW. Thereby, those three isolates were applied to explore their biodegradation ability in real world scenario. The biodegradation experiments showed that <em>Enterococcus faecium</em>, <em>Bacillus cereus</em>, and <em>Bacillus wiedmannii</em> were able to biodegrade hydrothermally treated CTLW at 98.67 %, 98.33 % and 98.00 %, respectively. The present study demonstrates <em>Enterococcus faecium</em>, <em>Bacillus cereus</em>, and <em>Bacillus wiedmannii</em> having biodegradation of CTLW applications might mitigate environmental pollution caused by this waste in the perspective of Bangladesh.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100479"},"PeriodicalIF":3.5,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143724548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Immunoinformatics-driven design of a multi-epitope vaccine against nipah virus: A promising approach for global health protection","authors":"Muhammad Aqib Shabbir ,&nbsp;Ammara Amin ,&nbsp;Ammarah Hasnain ,&nbsp;Ayesha Shakeel ,&nbsp;Ambreen Gul","doi":"10.1016/j.jgeb.2025.100482","DOIUrl":"10.1016/j.jgeb.2025.100482","url":null,"abstract":"<div><div>This study focuses on developing a multi-epitope vaccine against the highly pathogenic Nipah virus using immunoinformatics. It aims to design a vaccine targeting the viral nucleoprotein to elicit robust immune responses. The approach integrates epitope prediction, vaccine construction, and validation through computational tools to address the lack of effective vaccines and mitigate global health threats posed by Nipah virus outbreaks. Immunoinformatics approaches have been utilized for epitope prediction, focusing on B-cell and T-cell epitopes of the Nipah virus nucleoprotein. The multi-epitope vaccine was constructed using linkers and adjuvants to enhance immunogenicity. Structural refinement, molecular docking with human ephrin B2 receptor, and immune simulations were performed to validate the vaccine’s stability, binding efficiency, and immune response potential. The designed multi-epitope vaccine exhibited high antigenicity (0.56), non-allergenicity, and non-toxicity. Docking analysis showed a strong binding affinity with the ephrin B2 receptor (binding energy: −920 kcal/mol). Immune simulations indicated significant immune responses with high IgG and IgM levels and memory B-cell activation. Population coverage analysis revealed a global coverage of 88.3 %, supporting its potential for broad immunization. The designed vaccine against the Nipah virus demonstrates promising antigenicity, stability, and strong binding with the ephrin B2 receptor. With global population coverage and a robust immune response, it holds potential for clinical development. Further experimental validation and in vitro studies are recommended to confirm its efficacy as a viable vaccine candidate for the Nipah virus.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100482"},"PeriodicalIF":3.5,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143705868","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"What’s in (y)our food? − Occurrence of GM-containing foods on the Nigerian market and compliance with national regulations","authors":"Josephine Amedu ,&nbsp;Adedapo Adediji ,&nbsp;Ngozi Miracle ,&nbsp;Albert Anthony ,&nbsp;Precious Adeyemi ,&nbsp;Rabi Ahmed ,&nbsp;Stephen Atsumbe ,&nbsp;Mike Costly ,&nbsp;Ayodele Majekodunmi ,&nbsp;Odunayo Balogun ,&nbsp;Oyewumi Akinpelu ,&nbsp;Kilsi Borgbara ,&nbsp;Olanrewaju Olufowobi ,&nbsp;Hauwa Jibo Tahir ,&nbsp;Lukman Aroworamimo ,&nbsp;Agnes Asagbra","doi":"10.1016/j.jgeb.2025.100481","DOIUrl":"10.1016/j.jgeb.2025.100481","url":null,"abstract":"<div><div>The regulation of genetically modified (GM) food products in several jurisdictions considers appropriate labelling to be a key requirement for food safety and to ensure the protection of consumer choices. In Nigeria, such regulations are enforced by relevant government agencies. There is, however, little information on compliance levels with appropriate labeling regimes of GM products in Nigeria. This study was conducted to ascertain compliance with existing labeling guidelines and regulations for GM food products sampled from Abuja, Nigeria. DNA-based real-time polymerase chain reaction detection procedures were used to evaluate 15 processed and semi-processed pre-packaged food products obtained from retail stores in Abuja for the presence of specific regulatory sequences specific to GM products. Three regions present in GM food products were targeted, namely, the 35S promoter gene from cauliflower mosaic virus and figwort mosaic virus, with the nopaline synthase terminator from <em>Agrobacterium tumefaciens</em>. Eleven out of the 15 samples showed positive amplification for at least one regulatory sequence signature unique to GMOs, out of which only two were appropriately labeled as required by regulation. While the safety of GM products is a prerequisite for commercialization, labelling is required to protect consumer preference. The roles of relevant government agencies in developing appropriate labeling guidelines and enforcing the same to protect consumers’ choices are discussed.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100481"},"PeriodicalIF":3.5,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143697508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In silico exploration of biosynthetic gene clusters in marine Streptomyces sp. and Nocardiopsis sp. from the western coast of India: Genome-based profiling using whole genome sequencing","authors":"Hithesh Kumar ,&nbsp;Santhiya Vijayakumar ,&nbsp;Neha Shintre ,&nbsp;Vaijayanti Tamhane ,&nbsp;Neelima Deshpande ,&nbsp;Tushar Joshi ,&nbsp;Shalini Mathpal ,&nbsp;Anand Anbarasu ,&nbsp;Sudha Ramaiah","doi":"10.1016/j.jgeb.2025.100483","DOIUrl":"10.1016/j.jgeb.2025.100483","url":null,"abstract":"<div><div><em>Actinomycetes</em> are known for their ability to produce bioactive compounds with significant potency of antibiotics and natural product synthesis. With the growing threat of antimicrobial resistance, effective treatment for many infections has become increasingly challenging. Our study aims to explore the secondary metabolites produced by <em>Actinomycetes</em> isolated from marine sponge samples collected from the west coast of India using <em>in silico</em> approaches. The pre-processed high-throughput Illumina sequencing reads from six <em>Actinomycete</em> genomes showed high quality. Initial BLAST analysis followed by phylogenetic analysis revealed that isolates A01 and A96 closely matched <em>Nocardiopsis</em> sp., while isolates A03, A45, A57, and A90 were closely related to <em>Streptomyces</em> sp. <em>In silico</em> biosynthetic gene clusters (BGC) prediction indicated that <em>Streptomyces</em> sp. A57 had the highest number of BGCs, with 28 clusters identified. All <em>Streptomyces</em> sp. (A03, A45, A57, and A90) were predicted to contain a high number of terpene gene clusters. Ectoine was commonly found in all genomes of <em>Streptomyces</em> sp. and <em>Nocardiopsis</em> sp. Most of the BGCs identified in <em>Actinomycete</em> genomes revealed less similarity to the known BGCs, indicating their potential for producing novel secondary metabolites. The study reveals the genomic potential of the <em>Actinomycetes</em> by providing new insights into the ecological roles and potential applications of marine <em>Actinomycetes</em>, highlighting their promise as candidates for the discovery of new pharmaceuticals. Future investigations could benefit from integrating functional genomics and metabolomics to gain deeper insights into the metabolic pathways governing the biosynthesis of these secondary metabolites.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100483"},"PeriodicalIF":3.5,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143684833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}