3 Biotech最新文献

{"title":"Prospects of crude enzymes in replacing pure enzymes for dissolving pulp production","authors":"Prabhjot Kaur, Jitender Sharma, Nishi Kant Bhardwaj, Shubhang Bhardwaj, Daljeet Kaur, Amarjit Singh, Ashish Kumar","doi":"10.1007/s13205-024-04080-w","DOIUrl":"https://doi.org/10.1007/s13205-024-04080-w","url":null,"abstract":"<p>High-purity cellulose from paper pulp can be obtained after appropriate treatments involving pure xylanases and cellulases/endoglucanases. This study investigated the efficacy of using crude xylanase and cellulase instead of commercial ones to improve process economics. Kraft paper grade pulp produced from veneer waste, hardwood, and non-wood sources was utilized as a more sustainable option. Crude xylanase and cellulase from isolated soil bacteria <i>Bacillus pumilus</i> 3GAH and <i>Bacillus subtilis</i> PJK6 were used for process optimization. The correlation between Fock reactivity, chain scission, and crystallinity after crude-cellulase treatment was established through chemical, FTIR, and XRD analyses. Pentosans in kraft pulp were reduced from an initial 18.7% to 4.9% through sequential treatments with crude xylanase and alkali. Subsequent crude-cellulase treatment, even at 8 U/g o.d. pulp, improved Fock reactivity from 28.2% to 61.2%, fulfilling a major criterion for viscose. Thus, crude enzymes can be effectively used for the efficient and economical upgrading of paper pulp to dissolving pulp.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"68 1","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182826","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":"Fusarium begoniae metabolites: a promising larvicidal, pupicidal potential, histopathological alterations and detoxifications enzyme profiles of medically important mosquito vector Aedes aegypti, Culex quinquefasciatus and Anopheles stephensi","authors":"Chinnasamy Ragavendran, Annadurai Govindaraj, Chinnaperumal Kamaraj, Devarajan Natarajan, Guilherme Malafaia, Abdulwahed Fahad Alrefaei, Mikhlid H. Almutairi","doi":"10.1007/s13205-024-04061-z","DOIUrl":"https://doi.org/10.1007/s13205-024-04061-z","url":null,"abstract":"<p>Endophytic fungal molecules have the potential to be a cost-effective chemical source for developing eco-friendly disease-controlling pharmaceuticals that target mosquito-borne illnesses. The primary aims of the study were to identify the fungus <i>Fusarium begoniae</i> larvicidal ability against <i>Aedes aegypti</i>, <i>Culex quinquefasciatus,</i> and <i>Anopheles stephensi.</i> The ethyl acetate extract demonstrated lethal concentrations that kill 50% of exposed larvae (LC₅₀) and 90% of exposed larvae (LC₉₀) for the 1st to 4th instar larvae of <i>An. stephensi</i> (LC₅₀ = 54.821, 66.525, 68.250, and 73.614; LC₉₀ = 104.56, 138.205, 150.415, and 159.466 μg/mL), <i>Cx. quinquefasciatus</i> (LC₅₀ = 64.981, 36.505, 42.230, and 36.514; LC₉₀ = 180.46, 157.105, 140.318, and 153.366 μg/ mL), and <i>Ae. aegypti</i> (LC₅₀ = 74.890, 33.607, 52.173, and 26.974; LC₉₀ = 202.56, 162.205, 130.518, and 163.286 μg/mL). Mycelium metabolites were evaluated for their pupicidal activity towards <i>Ae. aegypti</i> (LC₅₀ = 80.669, LC₉₀ = 119.904), <i>Cx. quinquefasciatus</i> (LC₅₀ = 70.569, LC₉₀ = 109.840), and <i>An. stephensi</i> (LC₅₀ = 73.269, LC₉₀ = 110.590 μg/mL). The highest larvicidal activity was recorded at 300 µg/mL, with 100% mortality against first and second-instar larvae of <i>Cx. quinquefasciatus</i>. Metabolite exposure to larvae exhibited several abnormal behavioral changes. The exposure to <i>F. begoniae</i> metabolite, key esterases such as acetylcholinesterase, α-and-β-carboxylesterase, and acid and alkaline phosphatase activity significantly decreased compared to control larvae. The outcomes of the histology analysis revealed that the mycelium metabolites-treated targeted larvae had a disorganized abdominal mid and hindgut epithelial cells. The is first-hand information on study of ethyl-acetate-derived metabolites from <i>F. begoniae</i> tested against larvae and pupae of <i>Ae. aegypti, Cx. quinquefasciatus</i> and <i>An. stephensi</i>. Bio-indicator toxicity findings demonstrate that <i>A. nauplii</i> displayed no mortality.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"126 1","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142182840","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":"Deciphering the defense response in tomato against <i>Sclerotium rolfsii</i> by <i>Trichoderma asperellum</i> strain A10 through gene expression analysis.","authors":"C Shanmugaraj, Deeba Kamil, R Parimalan, Praveen Kumar Singh, P R Shashank, M A Iquebal, Zakir Hussain, Amrita Das, Robin Gogoi, K Nishmitha","doi":"10.1007/s13205-024-04040-4","DOIUrl":"10.1007/s13205-024-04040-4","url":null,"abstract":"<p><p>Biological control agents are preferred over chemicals for managing plant diseases, with <i>Trichoderma</i> species being particularly effective against soil-borne pathogens. This study examines the use of a highly antagonistic strain, <i>Trichoderma asperellum</i> A10, and a virulent strain, <i>Sclerotium rolfsii</i> Sr38, identified and confirmed through ITS, β-tubulin (<i>T. asperellum</i>), TEF 1α, and RPB2 (<i>S. rolfsii</i>) sequences. In vitro and in planta experiments compared the antagonistic potential of A10 with other antagonistic fungi and fungicides against <i>S. rolfsii</i>. A10 achieved 94.66% inhibition of <i>S. rolfsii</i> in dual culture assays. In greenhouse trials with tomato variety Pusa Ruby, A10 showed significant pre- and post-inoculation effectiveness, with disease inhibition of 86.17 and 80.60%, respectively, outperforming <i>T. harzianum</i>, Propiconazole, and Carbendazim. Additionally, microbial priming with A10 was explored to enhance plant defense responses. Pre-treatment of tomato plants with <i>T. asperellum</i> A10 led to significant upregulation of several defense-related genes, including PR1, PR2, PR3, PR5, PR12, thioredoxin peroxidase, catalase, polyphenol oxidase, phenylalanine ammonia lyase, isochorismate synthase, laccase, prosystemin, multicystatin, WRKY31, MYC2, lipoxygenase A, lipoxygenase C, proteinase inhibitor I, proteinase inhibitor II, and ethylene response 1 associated with various signaling pathways such as salicylic acid (SA)-mediated and jasmonic acid/ethylene (JA/ET)-mediated responses. This upregulation was particularly evident at 48 h post-inoculation in A10-primed plants challenged with <i>S. rolfsii</i>, inducing resistance against collar rot disease. This study underscores the effectiveness of <i>T. asperellum</i> A10 in controlling collar rot and highlights its potential for inducing resistance in plants through microbial priming, providing valuable insights into sustainable disease management strategies.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04040-4.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 9","pages":"210"},"PeriodicalIF":2.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11344752/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142071724","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 profiling and antibacterial activities of <i>Ziziphora tenuior</i> root extracts: a molecular docking against VanA of vancomycin-resistant enterococci.","authors":"Asma Hatami","doi":"10.1007/s13205-024-04056-w","DOIUrl":"10.1007/s13205-024-04056-w","url":null,"abstract":"<p><p>Medicinal plants, renowned for their antibacterial phytocompounds and secondary metabolites, hold significant promise in addressing antibiotic-resistant bacterial strains. This study aimed to conduct phytochemical profiling of the methanolic and dichloromethane extracts of <i>Ziziphora tenuior</i> root using the GC-MS technique. These extracts' antioxidant potential was assessed via DPPH assay and their antibacterial activity was evaluated against <i>S. aureus</i>, <i>E. coli</i>, and VRE bacterial strains. Furthermore, the drug-ligand interactions between the extracts' biocompounds and d-alanyl-d-lactate ligase (VanA) protein of vancomycin-resistant enterococci strains (VRE) were analyzed using molecular docking. Based on the results, 74% of methanolic extract consisted of (3methyl, 24S)-stigmast-5-en-3-ol (which is a β-sitosterol), followed by Tetrasiloxane, decamethyl (15.5%), and 1-methyl-4-phenyl-5-thioxo-1,2,4-triazolidin-3-one (10.5%). Also, the only predominant compound identified in the dichloromethane extract was Benzo[h]quinoline, 2,4-dimethyl-. Both extracts showed antioxidant activity, while the antioxidant activity of the methanolic extract (IC₅₀ = 95.33 μg/ml) was significantly higher than that of the dichloromethane extract (IC₅₀ = 934.23 μg/ml). Also, both extracts displayed substantial antibacterial efficacy against the tested pathogens, particularly against VRE. Moreover, the in silico analysis revealed that (3methyl, 24S)-stigmast-5-en-3-ol and Benzo[h]quinoline,2,4-dimethyl- exhibited notable interactions with VanA through docking energy values of - 9.0 and - 9.1 kcal/mol, respectively. Furthermore, these compounds formed 2 and 1 hydrogen bonds with VanA, respectively, highlighting their potential as effective interactants. These findings provide valuable visions into the therapeutic potentials of these plant-derived biocompounds in combating antibiotic-resistant bacterial infections.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 9","pages":"217"},"PeriodicalIF":2.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11362404/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103306","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":"Enhancement of the degradation capacity of <i>Is</i>PETase by acidic amino acids insertion and carbohydrate-binding module fusion.","authors":"Chuang Li, Qingqing Zheng, Wei Liu, Quanyu Zhao, Ling Jiang","doi":"10.1007/s13205-024-04041-3","DOIUrl":"10.1007/s13205-024-04041-3","url":null,"abstract":"<p><p>The biocatalytic degradation of poly(ethylene terephthalate) (PET) through enzymatic methods has garnered considerable attention due to its environmentally friendly and non-polluting nature, as well as its high specificity. While previous efforts in enhancing <i>Is</i>PETase performance have focused on amino acid substitutions in protein engineering, we introduced an amino acid insertion strategy in this work. By inserting a negatively charged acidic amino acid, Glu, at the right-angle bend of <i>Is</i>PETase, the binding capability between the enzyme's active pocket and PET was improved. The resulted mutant <i>Is</i>PETase^9394insE exhibited enhanced hydrolytic activity towards PET at various temperatures ranging from 30 to 45 ℃ compared with the wild-type <i>Is</i>PETase. Notably, a 10.04-fold increase was observed at 45 ℃. To further enhance PET hydrolysis, different carbohydrate-binding modules (CBMs) were incorporated at the C-terminus of <i>Is</i>PETase^9394insE. Among these, the fusion of CBM from <i>Verrucosispora sioxanthis</i> exhibited the highest enhancement, resulting in a 1.82-fold increase in PET hydrolytic activity at 37 ℃ compared with the <i>Is</i>PETase^9394insE. Finally, the engineered variant was successfully employed for the degradation of polyester filter cloth, demonstrating its promising hydrolytic capacity. In conclusion, this research presents an alternative enzyme engineering strategy for modifying PETases and enriches the pool of potential candidates for industrial PET degradation.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 9","pages":"195"},"PeriodicalIF":2.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11306670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141915855","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":"Genome-wide identification of <i>HSP90</i> gene family in <i>Rosa chinensis</i> and its response to salt and drought stresses.","authors":"Jun Xu, Shuangwei Liu, Yueming Ren, Yang You, Zhifang Wang, Yongqiang Zhang, Xinjie Zhu, Ping Hu","doi":"10.1007/s13205-024-04052-0","DOIUrl":"10.1007/s13205-024-04052-0","url":null,"abstract":"<p><p>Heat shock protein 90 (HSP90) is important for many organisms, including plants. Based on the whole genome information, the gene number, gene structure, evolutionary relationship, protein structure, and active site of the HSP90 gene family in <i>Rosa chinensis</i> and <i>Rubus idaeus</i> were determined, and the expression of the <i>HSP90</i> gene under salt, and drought stresses in two rose varieties Wangxifeng and Sweet Avalanche were analyzed. Six and eight <i>HSP90</i> genes were identified from <i>R. chinensis</i> and <i>Ru. idaeus</i>, respectively. Phylogenetic analysis revealed that the analyzed genes were divided into two Groups and four subgroups (Classes 1a, 1b, 2a, and 2b). Although members within the same classes displayed highly similar gene structures, while the gene structures and conserved domains of Group 1 (Class 1a and 1b) and the Group 2 (Class 2a and 2b) are different. Tandem and segmental duplication genes were found in <i>Ru. idaeus</i>, but not in <i>R. chinensis</i>, perhaps explaining the difference in <i>HSP90</i> gene quantity in the two analyzed species. Analysis of cis-acting elements revealed abundant abiotic stress, photolight-response, and hormone-response elements in <i>R. chinensis</i> HSP90s. qRT-PCR analysis suggested that <i>RcHSP90-1-1</i>, <i>RcHSP90-5-1</i> and <i>RcHSP90-6-1</i> in Sweet Avalanche and Wangxifeng varieties played important regulatory roles under salt and drought stress. The analysis of protein structure and active sites indicate that the potential different roles of <i>RcHSP90-1-1</i>, <i>RcHSP90-5-1</i>, and <i>RcHSP90-6-1</i> in salt and drought stresses may come from the differences of corresponding protein structures and activation sites. These data will provide information for the breeding of rose varieties with high stress resistance.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04052-0.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 9","pages":"204"},"PeriodicalIF":2.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11330952/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003327","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":"Advances in glycosyltransferase-mediated glycodiversification of small molecules.","authors":"Nguyen Huy Thuan, Quach Thi Thu Huong, Bui Dinh Lam, Ho Thanh Tam, Pham The Thu, Nguyen Xuan Canh, Vinay Bharadwaj Tatipamula","doi":"10.1007/s13205-024-04044-0","DOIUrl":"10.1007/s13205-024-04044-0","url":null,"abstract":"<p><p>Currently, numerous glycosides have been synthesized and used in clinical applications, neutraceuticals, cosmetics, and food processing. Structurally, a glycoside is composed of aglycone attaching to one or several sugar moieties so-called glycone. It is found that biochemical or biopharmaceutical properties of glycoside are mainly determined by its sugar part and thereby alternation of this glycone resulting in novel structure and characteristics as well. The use of traditional production methods of glycosides such as direct extraction and purification from plants, animals, or microorganisms is very challenging (laborious, time-consuming, technique, high price, low yield, etc.). Alternatively, the use of enzymatic methods for the biosynthesis of glycosides has become a highly promising tool. Particularly, the diverse structure of glycosides can be obtained using the promiscuous catalytic activity of glycosyltransferases (GT) mined from bioresources (plants, fungi, microorganisms, etc.). In addition, the exploration of GT catalytic promiscuity toward diverse aglycones, and glycones has indeed been interesting and played a key role in the production of novel glycosides. This review described the recent advances in glycosyltransferase-mediated glycodiversification of small molecules (flavonoids, steroids, terpenoids, etc.). Mostly, references were collected from 2014 to 2023.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 9","pages":"209"},"PeriodicalIF":2.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11343957/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142054629","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":"Consortia of <i>Streptomyces</i> spp. triggers defense/PAMP genes during the interaction of <i>Groundnut bud</i> <i>necrosis</i> <i>orthotospovirus</i> in tomato.","authors":"A S Rahul Dev, S Harish, G Karthikeyan, M Nivedha, C Sangeetha","doi":"10.1007/s13205-024-04030-6","DOIUrl":"10.1007/s13205-024-04030-6","url":null,"abstract":"<p><p>In the present study, <i>Streptomyces</i> spp. were isolated, characterized, and the efficacy was tested against <i>Groundnut bud necrosis orthotospovirus</i> (GBNV) in tomato. Among the three inoculation methods viz., pre-, post-, and simultaneous inoculation, tested for antiviral efficacy, pre-inoculation spray of the three <i>Streptomyces</i> spp. viz., <i>Streptomyces mutabilis, Streptomyces rochei,</i> and <i>Streptomyces chrestomyceticus</i> (SAT1, SAT4, and STR2) recorded the least disease severity index (DSI) of GBNV in tomato. In the pot culture, seed treatment of liquid consortium of three <i>Streptomyces</i> spp. @ 2 ml/g of seeds along with seedling dip at 10 ml/lit followed by soil drenching at 10 ml/lit on 7 days after transplanting (DAT) and foliar application at 0.5% on 15 DAT, 30 DAT, and 45 DAT recorded the least GBNV infection of 15% DSI and 16.67% DSI in trial I and II respectively. Besides, under field conditions, the disease incidence was reduced to 14.44% recording a higher yield of 76.67 t/ha in the treated plants against 63.99 t/ha in control. Upregulation of defense genes viz., PR1, PR2, PR6, WRKY, MAPKK, and NPR1 during tripartite interaction between tomato, <i>Streptomyces</i>, and GBNV was analyzed by qRTPCR, indicating that the consortia could decrease the virus severity through induced systemic resistance pathways. Thus, it is concluded that <i>Streptomyces</i> spp. can be used for the management of GBNV in tomato.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04030-6.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 9","pages":"196"},"PeriodicalIF":2.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11306705/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141915844","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":"Methyl Red degradation by a subseafloor fungus <i>Schizophyllum commune</i> 15R-5-F01: efficiency, pathway, and product toxicity.","authors":"Hui Xu, Hong-Ye Zheng, Chang-Hong Liu","doi":"10.1007/s13205-024-04037-z","DOIUrl":"10.1007/s13205-024-04037-z","url":null,"abstract":"<p><p>Synthetic dyes pose a significant environmental threat due to their complex structures and resistance to microbial degradation. <i>S. commune</i> 15R-5-F01 exhibited over 96% degradation efficiency of Methyl Red in a medium with 100 mg L^-1 Methyl Red within 3 h. The fungus demonstrated adaptability to various environmental conditions, including different pH levels, temperatures, oxygen concentrations, salinity, and heavy metals. <i>S. commune</i> 15R-5-F01 is capable of achieving repeated cycles of Methyl Red reduction with sustained degradation duration minimum of 6 cycles. It showed a maximum Methyl Red biodegradation capacity of at least 558 mg g^-1 dry mycelia and a bioadsorption capacity of 57 mg g^-1. Gas chromatography-mass spectrometry analysis confirmed the azo reduction of Methyl Red into N,N-dimethyl-p-phenylenediamine and 2-aminobenzoic acid. Enzymatic activity assays indicated the involvement of lignin peroxidases, laccases, and manganese peroxidase in the biodegradation process. Phytotoxicity tests on <i>Triticum eastivum</i>, <i>Oryza sativa</i>, and <i>Vigna umbellata</i> seeds revealed reduced toxicity of the degradation products compared to Methyl Red. This study identifies <i>S. commune</i> 15R-5-F01 as a viable candidate for the sustainable degradation of synthetic dyes in industrial wastewater.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 9","pages":"202"},"PeriodicalIF":2.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11327228/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141999250","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":"Computational exploration of protein structure dynamics and RNA structural consequences of <i>PKD1</i> missense variants: implications in ADPKD pathogenesis.","authors":"Chandra Devi, Prashant Ranjan, Sonam Raj, Parimal Das","doi":"10.1007/s13205-024-04057-9","DOIUrl":"10.1007/s13205-024-04057-9","url":null,"abstract":"<p><p>We analyzed the impact of nine previously identified missense <i>PKD1</i> variants from our studies, including c.6928G > A p.G2310R, c.8809G > A p.E2937K, c.2899 T > C p.W967R, c.6284A > G p.D2095G, c.6644G > A p.R2215Q, c.7810G > A p.D2604N, c.11249G > C p.R3750P, c.1001C > T p.T334M, and c.3101A > G p.N1034S on RNA structures and PC1 protein structure dynamics utilizing computational tools. RNA structure analysis was done using short RNA snippets of 41 nucleotides with the variant position at the 21st nucleotide, ensuring 20 bases on both sides. The secondary structures of these RNA snippets were predicted using RNAstructure. Structural changes of the mutants compared to the wild type were analyzed using the MutaRNA webserver. Molecular dynamics (MD) simulation of PC1 wild-type and mutant protein regions were performed using GROMACS 2018 (GROMOS96 54a7 force field). Findings revealed that five variants including c.8809G > A (p.E2937K), c.11249G > C (p.R3750P), c.3101A > G (p.N1034S), c.6928G > A (p.G2310R), c.6644G > A (p.R2215Q) exhibited major alterations in RNA structures and thereby their interactions with other proteins or RNAs affecting protein structure dynamics. While certain variants have minimal impact on RNA conformations, their observed alterations in MD simulations indicate impact on protein structure dynamics highlighting the importance of evaluating the functional consequences of genetic variants by considering both RNA and protein levels. The study also emphasizes that each missense variant exerts a unique impact on RNA stability, and protein structure dynamics, potentially contributing to the heterogeneous clinical manifestations and progression observed in Autosomal Dominant Polycystic Kidney Disease (ADPKD) patients offering a novel perspective in this direction. Thus, the utility of studying the structure dynamics through computational tools can help in prioritizing the variants for their functional implications, understanding the molecular mechanisms underlying variability in ADPKD presentation and developing targeted therapeutic interventions.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04057-9.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":"14 9","pages":"211"},"PeriodicalIF":2.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11344749/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142071723","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}