3 BiotechPub Date : 2025-01-01Epub Date: 2024-12-05DOI: 10.1007/s13205-024-04165-6
Xinming Feng, Xinyu Cui, Kun Wang, Juanjuan Liu, Dongdong Meng
{"title":"Enzymatic characterization of a thermostable 6-phosphogluconate dehydrogenase from <i>Hydrogenobacter thermophilus</i> and its application for NADH regeneration.","authors":"Xinming Feng, Xinyu Cui, Kun Wang, Juanjuan Liu, Dongdong Meng","doi":"10.1007/s13205-024-04165-6","DOIUrl":"10.1007/s13205-024-04165-6","url":null,"abstract":"<p><p>6-Phosphogluconate dehydrogenases (6PGDHs) are widely existing as reduced cofactor (NADH/NADPH) regeneration biocatalysts. Herein, a thermostable 6PGDH from <i>Hydrogenobacter thermophilus</i> (Ht6PGDH) was overexpressed in <i>Escherichia coli</i> and enzymologically characterized. Ht6PGDH exhibited exceptional stability and catalytic activity under high-temperature conditions, with an optimum temperature of 85 °C and the ability to maintain high activity for prolonged periods at 70 °C, which could be purified through a one-step heat treatment. Moreover, Ht6PGDH exhibited a preference for NAD<sup>+</sup> with a <i>K</i> <sub>m</sub> value of 0.4 mM and a <i>k</i> <sub>cat</sub> value of 28.6 s⁻<sup>1</sup>, demonstrating a significant preference over NADP<sup>+</sup>. These properties render Ht6PGDH a potentially valuable enzyme for high-temperature bioconversion and in vitro synthetic biosystems. Additional research showed that Ht6PGDH excelled in the regeneration of NADH, achieving efficient lactate production when integrated into an in vitro synthetic biosystem containing lactate dehydrogenase (LDH). Furthermore, the cascade reaction of Ht6PGDH with glucose-6-phosphate dehydrogenase (G6PDH) was explored for NADH regeneration using starch as the substrate, further validating its potential application in complex biosynthetic systems.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04165-6.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"15 1","pages":"3"},"PeriodicalIF":2.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11621248/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142798944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Journal of biomechanicsPub Date : 2025-01-01Epub Date: 2024-08-30DOI: 10.1016/j.jbiomech.2024.112299
M Fernandes, L C Sousa, C C António, S Silva, S I S Pinto
{"title":"A review of computational methodologies to predict the fractional flow reserve in coronary arteries with stenosis.","authors":"M Fernandes, L C Sousa, C C António, S Silva, S I S Pinto","doi":"10.1016/j.jbiomech.2024.112299","DOIUrl":"10.1016/j.jbiomech.2024.112299","url":null,"abstract":"<p><p>Computational methodologies for predicting the fractional flow reserve (FFR) in coronary arteries with stenosis have gained significant attention due to their potential impact on healthcare outcomes. Coronary artery disease is a leading cause of mortality worldwide, prompting the need for accurate diagnostic and treatment approaches. The use of medical image-based anatomical vascular geometries in computational fluid dynamics (CFD) simulations to evaluate the hemodynamics has emerged as a promising tool in the medical field. This comprehensive review aims to explore the state-of-the-art computational methodologies focusing on the possible considerations. Key aspects include the rheology of blood, boundary conditions, fluid-structure interaction (FSI) between blood and the arterial wall, and multiscale modelling (MM) of stenosis. Through an in-depth analysis of the literature, the goal is to obtain an overview of the major achievements regarding non-invasive methods to compute FFR and to identify existing gaps and challenges that inform further advances in the field. This research has the major objective of improving the current diagnostic capabilities and enhancing patient care in the context of cardiovascular diseases.</p>","PeriodicalId":15168,"journal":{"name":"Journal of biomechanics","volume":" ","pages":"112299"},"PeriodicalIF":2.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Journal of biomechanicsPub Date : 2025-01-01Epub Date: 2024-09-04DOI: 10.1016/j.jbiomech.2024.112297
Felipe Sempértegui, Stéphane Avril
{"title":"Integration of cross-links, discrete fiber distributions and of a non-local theory in the Homogenized Constrained Mixture Model to Simulate Patient-Specific Thoracic Aortic Aneurysm Progression.","authors":"Felipe Sempértegui, Stéphane Avril","doi":"10.1016/j.jbiomech.2024.112297","DOIUrl":"10.1016/j.jbiomech.2024.112297","url":null,"abstract":"<p><p>Thoracic aortic aneurysms (TAA) represent a critical health issue for which computational models can significantly contribute to better understand the physiopathology. Among different computational frameworks, the Homogenized Constrained Mixture Theory has shown to be a computationally efficient option, allowing the inclusion of several mechanically significant constituents into a layer-specific mixture. Different patient-specific Growth and Remodeling (G&R) models correctly predicted TAA progression, although simplifications such as the inclusion of a limited number of collagen fibers and imposed boundary conditions might limit extensive analyses. The current study aims to enhance existing models by incorporating several discrete collagen fibers and to remove restrictive boundary conditions of the previous models. The implementation of discretized fiber dispersion presents a more realistic description of the vessel, while the removal of boundary conditions was addressed by including cross-links in the model to provide a supplemental stiffness against through-thickness shearing, a feature that was previously absent, and by the development of a non-local framework that ensures the stable deposition and degradation of collagen fibers. With these improvements, the current model represents a step forward towards more robust and comprehensive simulations of TAA growth.</p>","PeriodicalId":15168,"journal":{"name":"Journal of biomechanics","volume":" ","pages":"112297"},"PeriodicalIF":2.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142145715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
3 BiotechPub Date : 2025-01-01Epub Date: 2024-12-12DOI: 10.1007/s13205-024-04180-7
Leyao Fang, Junxi Shen, Yi Wu, Zhoujin Tan
{"title":"Involvement of intestinal mucosal microbiota in adenine-induced liver function injury.","authors":"Leyao Fang, Junxi Shen, Yi Wu, Zhoujin Tan","doi":"10.1007/s13205-024-04180-7","DOIUrl":"10.1007/s13205-024-04180-7","url":null,"abstract":"<p><p>Adenine is frequently utilized as a model medication for chronic renal disease. Adenine can affect organs other than the kidneys, including the heart and the intestine. The liver is a vital organ involved in the in vivo metabolism of adenine. Adenine may negatively impact liver function. Research indicated that adenine caused dysbiosis of the gut microbiota in mice. Investigations into the gut-liver axis have demonstrated a substantial association between drug-induced hepatic dysfunction and gut microbiota. Consequently, we delivered distinct dosages of adenine via gavage to mice to examine the correlation between adenine-induced liver impairment and gut microbiota dysbiosis. Mice were treated with low-dose adenine suspension (NLA), medium-dose adenine suspension (NMA), high-dose adenine suspension (NHA), and sterile water (NC) as a control. The results indicated that mice in the NLA, NMA, and NHA groups had decreased body weight and a reduction in liver index. Subsequent to adenine administration, the concentrations of AST, ALT, and LDH increased, whereas SDH levels decreased. As doses increased, liver function impairment and hepatic energy metabolism abnormalities aggravated. Adenine also damaged the colonic architecture in mice. Moreover, adenine modified the makeup and structure of the gut mucosal microbiota, enhancing specific bacterial genera and influencing the microbiota's energy metabolism-related functions. The results of our research established a correlation among certain bacteria, liver function injury, and hepatic energy metabolism. The gut mucosal microbiota was involved in adenine-induced liver injury and hepatic energy metabolism. These results can offer novel insights into the role of gut microbiota in drug-induced liver injury and provide specific guidelines for the modeling and therapeutic application of adenine.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"15 1","pages":"6"},"PeriodicalIF":2.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11638458/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142827192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jin Lee, Hyun-Ah Park, Kyung-Chul Shin, Deok-Kun Oh
{"title":"Bioconversion of eicosapentaenoic acid into 5S,15S- and 5R,15R-dihydroxyeicosapentaenoic acids by double-dioxygenating 15S- and 15R-lipoxygenases.","authors":"Jin Lee, Hyun-Ah Park, Kyung-Chul Shin, Deok-Kun Oh","doi":"10.1016/j.jbiosc.2024.09.002","DOIUrl":"10.1016/j.jbiosc.2024.09.002","url":null,"abstract":"<p><p>Resolvin E series (Rvs), such as RvE4 (5S,15S-dihydroxyeicosapentaenoic acid) and its stereoselective enantiomer (5R,15R-dihydroxyeicosapentaenoic acid), play an important role in promoting the resolution of inflammation and are derived from eicosapentaenoic acid (EPA) by M2 macrophage in human. However, they have been synthesized using expensive and inefficient chemical methods. Here, we performed efficient quantitative production of RvE4 and its enantiomer from EPA using Escherichia coli expressing double-dioxygenating 15S-lipoxygenase (15S-LOX) from Archangium violaceum and double-dioxygenating 15R-LOX from Sorangium cellulosum, respectively, with solvent, polymer, and adsorbent resin. The cell density, substrate concentration, solvent types and concentrations, polymer types and concentrations, and resin concentration were optimized for the enhanced bioconversion of EPA into RvE4 and its enantiomer. Under the optimized conditions, A. violaceum 15S-LOX and S. cellulosum 15R-LOX expressed in E. coli converted 6.0 mM EPA into 4.3 mM (1.44 g/L) RvE4 and 5.8 mM (1.94 g/L) RvE4 enantiomer in 60 min, with productivities of 4.3 and 5.8 mM/h and molar conversions of 72% and 97%, respectively. To date, these are the highest concentrations, productivities, and conversions of RvE4 and its enantiomer. The concentrations of RvE4 and its enantiomer obtained from the conversion of EPA with solvent, polymer, and resin were 2.5- and 3.2-fold higher than those without the additives, respectively.</p>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":" ","pages":"1-6"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142466296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Aromatic residues in the oligonucleotide binding domain are essential to the function of the single-stranded DNA binding protein of Helicobacter pylori.","authors":"Mon-Juan Lee, Li-Kun Huang, Wen-Hsin Huang, Po-Yu Chan, Zi-Sin Yang, Ching-Ming Chien, Ching-Chang Chieng, Haimei Huang","doi":"10.1016/j.jbiosc.2024.09.003","DOIUrl":"10.1016/j.jbiosc.2024.09.003","url":null,"abstract":"<p><p>Single-stranded DNA-binding protein (SSB) is essential to DNA replication, DNA repair, and homologous genetic recombination. Our previous study on the crystal structure of a C-terminally truncated SSB from Helicobacter pylori, HpSSBc, in complex with single-stranded DNA (ssDNA) suggests that several aromatic residues, including Phe37, Phe50, Phe56, and Trp84, were involved in ssDNA binding. To investigate the importance of these aromatic residues, the binding activity of four site-directed HpSSB mutants, including F37A HpSSB, F50A HpSSB, F56A HpSSB, and W84A HpSSB, was compared to that of wild-type HpSSB and HpSSBc by means of electrophoresis mobility shift assay (EMSA), tryptophan quenching fluorescence titration, and surface plasmon resonance (SPR). Molecular docking and molecular dynamic (MD) simulation of a F37A and a quadruple mutation model of HpSSBc support that the ssDNA-HpSSBc complex was destabilized when either one or four of the aromatic residues were mutated. The findings of this study suggest that mutation of the phenylalanine and tryptophan residues within the oligonucleotide-binding domain significantly diminished the ssDNA binding capability of HpSSB, highlighting the crucial role these aromatic residues play in the binding of ssDNA by HpSSB.</p>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":" ","pages":"7-13"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142568681","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Isolation, structure analysis and expression characterization of the Hexokinase gene family in <i>Sorghum bicolor</i>.","authors":"Sen Li, Yansheng Liu, Xin'er Qin, Xiaofei He, Shaopeng Han, Yang Lv, Zhuying Deng, Gongjian Zeng, Xinqiang Gao, Yongfeng Hu, Xiangling Shen","doi":"10.1007/s13205-024-04190-5","DOIUrl":"https://doi.org/10.1007/s13205-024-04190-5","url":null,"abstract":"<p><p>Hexokinases (HXK) not only facilitate carbohydrate metabolism but also play important roles in sugar sensing in higher plants. <i>HXK</i> gene families have been extensively discussed in many plant species; however, comprehensive information regarding <i>HXKs</i> in sorghum remains unclear. To address this gap, we identified 7 putative sorghum <i>HXKs</i> (<i>SbHXK1</i> to <i>SbHXK7</i>), and the features of their conserved domains, gene structure, evolutionary tree, and cis-acting elements were systematically characterized to reveal the evolutionary conservation between different plant species. Based on expression profiling, we found that different expression patterns of <i>SbHXKs</i> were associated with different physiological processes, including abiotic stresses. Further qRT-PCR verification under salt and sucrose treatment confirmed that <i>SbHXK2</i>, <i>SbHXK4</i>, and <i>SbHXK5</i> may play very important roles under high osmotic pressure. Notably, SbHXKs are predominantly localized in the cytoplasm, in contrast to some rice and <i>Arabidopsis</i> HXKs, which are localized in chloroplasts or mitochondria, suggesting divergent roles for SbHXKs. In summary, our study provides a theoretical foundation for understanding the HXK gene family and offers fundamental insights of <i>SbHXKs</i> in sorghum.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04190-5.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"15 1","pages":"20"},"PeriodicalIF":2.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11662118/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875815","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Phytochemical composition, in vitro cytotoxicity and in silico ADME/Tox analysis of the active compounds of <i>Oxalis latifolia</i> Kunth. extracts with promising anticancer potential.","authors":"Arumugam Vignesh, Karuppasamy Dharani, Subramaniam Selvakumar, Krishnan Vasanth","doi":"10.1007/s13205-024-04167-4","DOIUrl":"https://doi.org/10.1007/s13205-024-04167-4","url":null,"abstract":"<p><p>This study investigated the anticancer phytocompounds in leaf extracts of <i>Oxalis latifolia</i> Kunth. Quantitative analysis of the phytochemical composition showed high levels of primary metabolites: carbohydrates (45.11 ± 2.15 GLE mg/100 mg), proteins (28.13 ± 0.94 BSA mg/100 mg), and amino acids (13.25 ± 1.16 LE mg/100 mg). Ethyl acetate extracts had the highest concentrations of secondary metabolites, including phenolic content (122.52 ± 4.27 GAE mg/100 mg), total flavonoids (91.86 ± 2.65 QE mg/100 mg), and alkaloids (82.18 ± 0.72 COLE mg/100 mg). In addition, strong antioxidant activities were observed in the DPPH<sup>•</sup> scavenging assay (IC<sub>50</sub> 11.51 ± 2.28 µg/mL), ABTS<sup>·+</sup> radical cation scavenging activity (97.42 ± 7.19 µM TE/g), and FRAP assay (14.34 ± 1.24 mM Fe(II)/mg). Based on preliminary analysis, the ethyl acetate extract was fractionated using thin-layer chromatography (TLC), yielding two distinct fractions with Rf values of 0.31 and 0.76. GC-MS analysis of these fractions identified 33 bioactive compounds. These fractions exhibited anticancer activity against the A549 lung cancer cell line, with IC<sub>50</sub> values of 47.25 µg/mL and 48.31 µg/mL, as determined by the MTT assay. Furthermore, absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies on 25 selected compounds indicated favorable pharmacokinetic properties and drug-likeness. In silico molecular docking showed strong binding affinities of these bioactive compounds to the p21 protein, comparable to the synthetic drug Cisplatin-quercetin. The results highlight the potential of <i>O. latifolia</i> in anticancer therapy, particularly through modulation of the p21 pathway, supported by in vitro cytotoxicity assessments, molecular docking, and ADMET analysis.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04167-4.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"15 1","pages":"19"},"PeriodicalIF":2.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11662119/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dental MaterialsPub Date : 2025-01-01Epub Date: 2024-11-02DOI: 10.1016/j.dental.2024.10.012
Julia Fehrenbach, Jéssica Lopes Soares de Soares, João Carlos Silva do Nascimento Foly, Leonardo Lamberti Miotti, Eliseu Aldrighi Münchow
{"title":"Mechanical performance of endocrown restorations in anterior teeth: A systematic review and network meta-analysis.","authors":"Julia Fehrenbach, Jéssica Lopes Soares de Soares, João Carlos Silva do Nascimento Foly, Leonardo Lamberti Miotti, Eliseu Aldrighi Münchow","doi":"10.1016/j.dental.2024.10.012","DOIUrl":"10.1016/j.dental.2024.10.012","url":null,"abstract":"<p><strong>Objectives: </strong>To conduct a systematic review and network meta-analysis (NMA) to answer whether endocrown restorations have similar mechanical behavior than other traditional core-crown systems with or without intracanal posts for the rehabilitation of anterior endodontically treated teeth.</p><p><strong>Methods: </strong>The review followed the PRISMA Extension Statement for NMA. Studies were identified by a systematic search to select reports on endocrown restorations in anterior teeth. A search was performed in PubMed (MEDLINE), Scopus, Web of Science, Embase, SciELO, and LILACS databases. Articles evaluating mechanical performance through in vitro and finite element analysis (FEA) studies were selected and the risk of bias was assessed using the RoBDEMAT and ROBFEAD tools, respectively. The data were analyzed qualitatively and quantitatively through NMA using the MetaInsight tool.</p><p><strong>Results: </strong>Eleven articles were included (eight in vitro and three with FEA design). Six in vitro studies were evaluated using NMA. Composite resin endocrowns showed greater load-to-fracture and lower occurrence of catastrophic failures than traditional restorations. Combining glass fiber post with composite restoration also showed good strength behavior. Regarding FEA studies, two out of three studies showed a more homogeneous distribution of stress for the endocrown group.</p><p><strong>Significance: </strong>Endocrowns performed similarly to or better than conventional restorative strategies, with composite resin being the most recommended material of choice. The rehabilitation of endodontically treated anterior teeth with extensive coronal destruction is typically challenging for the dentist, and there is still no consensus in the literature that provides conclusive answers for choosing the appropriate material and restorative strategy. Exploring new techniques and materials that make this procedure easier for the dentist and guarantee good results is paramount.</p>","PeriodicalId":298,"journal":{"name":"Dental Materials","volume":" ","pages":"28-41"},"PeriodicalIF":4.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142566852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
3 BiotechPub Date : 2025-01-01Epub Date: 2024-12-15DOI: 10.1007/s13205-024-04172-7
Pedro Marcus Pereira Vidigal, Humberto Moreira Hungaro
{"title":"Genome sequencing of <i>Escherichia coli</i> phage <i>UFJF_EcSW4</i> reveals a novel lytic <i>Kayfunavirus</i> species.","authors":"Pedro Marcus Pereira Vidigal, Humberto Moreira Hungaro","doi":"10.1007/s13205-024-04172-7","DOIUrl":"https://doi.org/10.1007/s13205-024-04172-7","url":null,"abstract":"<p><p>The <i>Escherichia coli</i> phage <i>UFJF_EcSW4</i> was isolated from polluted stream water and showed clear lysis plaques on the host, measuring 0.67 ± 0.43 mm, with a titer of 9.57 ± 0.23 log PFU/ml. It demonstrated a very narrow host range, infecting only its host. Additionally, it has a short latent period of 9 min, a burst size of 49 PFU/infected cell, and stability over a wide range of pH, temperature, and free residual chlorine. The phage has a double-stranded DNA genome spanning 40,299 bp, with a GC content of 49.87% and short-direct terminal repeats (DTR) sequences of 286 bp. The <i>UFJF_EcSW4</i> genome contains 55 genes, organized into functional modules with a unidirectional arrangement, regulated by 22 promoters (three from the phage and 19 from the host) and three Rho-independent terminators. Comparative analysis revealed that the <i>UFJF_EcSW4</i> genome shares an average genomic similarity of 77.82% with the genome sequences of phages from the <i>Kayfunavirus</i> genus but does not surpass the 95% threshold necessary for species classification. Therefore, the <i>UFJF_EcSW4</i> is a novel <i>Kayfunavirus UFJF_EcSW4</i> species belonging to the <i>Studiervirinae</i> subfamily.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04172-7.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"15 1","pages":"10"},"PeriodicalIF":2.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11646959/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}