Biotechnology Letters最新文献

{"title":"Efficient RNA interference method by feeding in Brachionus plicatilis (Rotifera).","authors":"Yu Zhang, Dongqi Kan, Yang Zhou, Hairong Lian, Lingling Ge, Jing Shen, Zhongqi Dai, Yan Shi, Cui Han, Xiaojie Liu, Jiaxin Yang","doi":"10.1007/s10529-024-03524-w","DOIUrl":"10.1007/s10529-024-03524-w","url":null,"abstract":"<p><p>Rotifers are small, ubiquitous invertebrate animals found throughout the world and have emerged as a promising model system for studying molecular mechanisms in the fields of experimental ecology, aquatic toxicology, and geroscience. However, the lack of efficient gene expression manipulation techniques has hindered the study of rotifers. In this study, we used the L4440 plasmid with two reverse-oriented T7 promoters, along with RNase-deficient E. coli HT115, to efficiently produce dsRNA and thereby present an efficient feeding-based RNAi method in Brachionus plicatilis. We targeted Bp-Ku70 & Ku80, key proteins in the DNA double-strand breaks repair pathway, and then subjected rotifers to UV radiation. We found that the mRNA expression, fecundity, as well as survival rate diminished significantly as a result of RNAi. Overall, our results demonstrate that the feeding-based RNAi method is a simple and efficient tool for gene knockdown in B. plicatilis, advancing their use as a model organism for biological research.</p>","PeriodicalId":8929,"journal":{"name":"Biotechnology Letters","volume":" ","pages":"961-971"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142131747","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":"Rolling circle amplification cooperating crRNA switch for direct and sensitive methicillin-resistant Staphylococcus aureus (MRSA) analysis.","authors":"Junling Qiu, Chang Liu, Yuxia Zhu","doi":"10.1007/s10529-024-03550-8","DOIUrl":"https://doi.org/10.1007/s10529-024-03550-8","url":null,"abstract":"<p><p>Evaluating the methicillin resistance of Staphylococcus aureus (S. aureus) is highly important for adapting nursing strategies. Nevertheless, the identification of methicillin-resistant S. aureus (MRSA) that is both sensitive and reliable continues to pose a significant obstacle. This study describes a method for detecting MRSA using a combination of fixed rolling circle amplification (RCA) and the exonuclease-iii (Exo-iii) assisted CRISPR-Cas12a system for signal amplification. When MRSA is present, the interaction between the \"b\" chain in the capture probe and MRSA allows the \"a\" chain to be exposed. This \"a\" chain acts as a primer to initiate the fixed RCA process. The H probe, which includes the crRNA segment, forms a bond with the RCA product and then releases the crRNA segment with the aid of Exo-iii. The Cas12a protein, when combined with the crRNA, generates an activated CRISPR-Cas12a system that cleaves the \"Reporter\" probe, resulting in the production of fluorescent signals. Furthermore, this fluorescent test has been utilized for the examination of clinical samples with a satisfactory rate of retrieval. Based on the elegant design, the proposed method exhibited a low detection limit of 4.6 cfu/mL, while maintaining a high specificity for MRSA even from a mixture of several interfering bacteria. Due to its cost-effectiveness, simplicity, and adaptability, the sensing system shows potential as a platform for detecting MRSA and evaluating postoperative nursing for stomach cancer patients.</p>","PeriodicalId":8929,"journal":{"name":"Biotechnology Letters","volume":"47 1","pages":"4"},"PeriodicalIF":2.0,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142708971","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":"Butea monosperma bark extract: a natural boost for osteogenesis via Wnt/β-catenin pathway activation in adipose-derived mesenchymal stem cells.","authors":"Rebu Sundar, Gayathri Sundar, Annie John, Annie Abraham","doi":"10.1007/s10529-024-03545-5","DOIUrl":"https://doi.org/10.1007/s10529-024-03545-5","url":null,"abstract":"<p><strong>Purpose: </strong>To investigate the impact of Butea monosperma (BM) bark extract on the osteogenic differentiation potential of rat adipose-derived mesenchymal stem cells (rADMSCs) and to elucidate the involvement of Wnt/β-catenin pathway in mediating this osseous effect.</p><p><strong>Methods: </strong>Characterizations (antioxidant assays, FTIR and LC/MS analyses) and docking studies (in silico) were performed to evaluate the presence of phytochemicals in the BM extract and their binding capacity to that of the frizzled receptor. rADMSCs were isolated and characterised for its differentiation potential of osteogenesis for stemness. Dose fixation, cytotoxicity, osteogenic differentiation (calcium, mineral deposition, alkaline phosphatase and osteocalcin) and gene expression (osteocalcin, Col1, osteonectin, Bmp2, Runx2, Wnt2, and β-catenin-14 and 28 days) of the extract were also evaluated in vitro.</p><p><strong>Results: </strong>FTIR and LC/MS analyses unveiled the phytochemicals in the extract and with docking studies confirmed their interaction with the frizzled receptor of Wnt/β-catenin pathway. rADMSCs were isolated and differentiated in the presence of the osteogenic induction medium. Dose fixation studies, cytotoxicity and cell viability assessments demonstrated the phytochemicals concentration-dependent cytotoxicity. The presence of specific bone markers highlighted the osteogenic differentiation potential of the phytochemicals. Furthermore, gene expression studies of rADMSCs depicted a heightened bone-forming capacity potentially facilitated by the activation of Wnt/β-catenin pathway.</p><p><strong>Conclusion: </strong> The phytochemicals of BM promoted the osteogenic differentiation of rADMSCs through the activation of the signalling Wnt/β-Catenin pathway, as evidenced by the significant upregulation of early and late bone markers. The phytochemicals may therefore be positioned as promising therapeutic agents for enhancing bone regeneration, offering new avenues for regenerative medicine.</p>","PeriodicalId":8929,"journal":{"name":"Biotechnology Letters","volume":"47 1","pages":"3"},"PeriodicalIF":2.0,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142708964","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":"Computer-aided rational design of a mRNA vaccine against Guanarito mammarenavirus.","authors":"Mohibullah Shah, Asifa Sarfraz, Muhammad Shehroz, Asia Perveen, Samavia Jaan, Aqal Zaman, Umar Nishan, Arlindo A Moura, Riaz Ullah, Zafar Iqbal, Mohamed A Ibrahim","doi":"10.1007/s10529-024-03543-7","DOIUrl":"https://doi.org/10.1007/s10529-024-03543-7","url":null,"abstract":"<p><strong>Purpose: </strong>Guanarito mammarenavirus (GTOV) is a highly pathogenic virus that leads to Venezuelan hemorrhagic fever (VHF). Despite being a severe disease, there are currently no commercially available drugs or vaccines for its prevention.</p><p><strong>Methods: </strong>Here we computationally formulated a mRNA vaccine construct (VC) from the genome of GTOV to produce immunity against its infections. Two proteins, namely zinc-finger motif protein (NP_899220.1), and nucleocapsid protein (NP_899211.1) were screened as potential candidates for downstream analysis.</p><p><strong>Results: </strong>We determined the T and B cell epitopes of the candidate proteins. The resulting epitopes were analyzed, and the best epitopes were utilized in the formation of the peptide vaccine construct. The secondary and tertiary structures of the peptide construct were predicted and validated. Docking was conducted to check the binding energy of the designed peptide vaccine with the human immune receptors, namely TLR2 and TLR4. Our designed vaccine showed stable interactions with the HLA molecules, as verified through normal mode and MD simulation analysis. The immune simulation results indicated a positive immune response against the construct. A potentially stable mRNA vaccine was formulated by adding of sequences such as the Kozak, Goblin 5' UTR, tPA-signal peptide, MITD, 3' UTRs, and a poly(A) tail to the peptide vaccine construct. Lastly, the expression probability of the mRNA vaccine was confirmed in the expression system of E. coli strain K12.</p><p><strong>Conclusion: </strong>The designed vaccine showed the potential to elicit an immune response against the GTOV infection; however, experimental validation is recommended to verify the in-silico findings of this study.</p>","PeriodicalId":8929,"journal":{"name":"Biotechnology Letters","volume":"47 1","pages":"2"},"PeriodicalIF":2.0,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142708966","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":"Production of derivatives of α-terpineol by bacterial CYP102A1 enzymes.","authors":"Jeong-Hoon Kim, Chan Mi Park, Hae Chan Jeong, Sungbeom Lee, Chul-Ho Yun","doi":"10.1007/s10529-024-03540-w","DOIUrl":"https://doi.org/10.1007/s10529-024-03540-w","url":null,"abstract":"<p><p>The monooxygenase activity of engineered CYP102A1 on α-terpineol was investigated. CYP102A1 M850 mutant (F11Y/R47L/D68G/F81I/F87V/E143G/L188Q/E267V/H408R) showed the highest catalytic activity toward α-terpineol among the engineered mutants produced by random mutagenesis. The major product (P1) of α-terpineol, p-menth-1-ene-3,8-diol, was characterized by high-performance liquid chromatography, gas-chromatography mass spectrometry, and nuclear magnetic resonance spectroscopy. Three minor products (P2-P4) of α-terpineol were considered as 6-hydroxy-α,α,4-trimethyl-3-cyclohexene-1-methanol (P2), trans-sobrerol (P3), and carvone hydrate (P4). Optimal conditions for product formation were determined as pH 7.0 and 30 °C. Production of p-menth-1-ene-3,8-diol was 0.87 mM at 1 h. Structure modeling using PyMOL and CAVER Web 1.2 server indicated that several mutations of CYP102A1 M850 were involved in access tunnels and active sites, resulting in increased activity toward α-terpineol. The major product, p-menth-1-ene-3,8-diol, of α-terpineol was produced by engineered CYP102A1 M850 via regioselective carbon hydroxylation. The engineered CYP102A1 could be a suitable biocatalyst for producing α-terpineol derivatives.</p>","PeriodicalId":8929,"journal":{"name":"Biotechnology Letters","volume":"47 1","pages":"1"},"PeriodicalIF":2.0,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142708970","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":"Preparation of white rot fungal inoculum and its application to bioremediation of chlorimuron-ethyl-contaminated soil.","authors":"Xiangyu Shi, Xin Wang, Ling Ge, Wenrui Liu, Mengqin Yao, Jia Bao","doi":"10.1007/s10529-024-03497-w","DOIUrl":"10.1007/s10529-024-03497-w","url":null,"abstract":"<p><p>Chlorimuron-ethyl is currently the primary herbicide used for chemical weed control in a soybean field. In this study, a solid microbial inoculum (corn stalk-white rot fungus (W-1)) was prepared for the remediation of farmland soil contaminated by chlorimuron-ethyl. Firstly, the preparation method of the microbial inoculum was studied. Secondly, the degradation rate of the chlorimuron-ethyl in the ground by the solid microbial inoculum is improved by optimizing the proportion of the protective agent. Then the effects of applying solid microbial inoculum, free bacteria and corn straw on the degradation rate of chlorimuron-ethyl in soil were weighed. Finally, Illumina MiSeq sequencing was used to measure the composition and diversity of bacterial and fungal communities in the ground before and after using microbial inoculum. The degradation rate of chlorimuron-ethyl in soil by solid microbial inoculum was 84.87% after 20 d using corn straw as the support, room temperature drying, 4% Ca₃(PO₄)₂ as the protective drying agent, and 1%(w) dextrin as the ultraviolet protective agent. Inoculation of white rot fungi could significantly affect the community structure of bacteria and fungi in the soil, making the chlorimuron-ethyl degrading communities become the dominant communities and playing an essential role in the degradation of chlorimuron-ethyl. The results showed that using solid microbial inoculum was an effective way to repair farmland soil polluted by chlorimuron-ethyl.</p>","PeriodicalId":8929,"journal":{"name":"Biotechnology Letters","volume":" ","pages":"767-780"},"PeriodicalIF":2.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141282894","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":"Proteome profiling, biochemical and histological analysis of diclofenac-induced liver toxicity in Yersinia enterocolitica and Lactobacillus fermentum fed rat model: a comparative analysis.","authors":"Shruti Ahlawat, Hari Mohan, Krishna Kant Sharma","doi":"10.1007/s10529-024-03510-2","DOIUrl":"10.1007/s10529-024-03510-2","url":null,"abstract":"<p><p>Diclofenac is a hepatotoxic non-steroidal anti-inflammatory drug (NSAID) that affects liver histology and its protein expression levels. Here, we studied the effect of diclofenac on rat liver when co-administrated with either Yersinia enterocolitica strain 8081 serotype O:8 biovar 1B (D*Y) or Lactobacillus fermentum strain 9338 (D*L). Spectroscopic analysis of stool samples showed biotransformation of diclofenac. When compared with each other, D*Y rats lack peaks at 1709 and 1198 cm^-1, while D*L rats lack peaks at 1411 cm^-1. However, when compared to control, both groups lack peaks at 1379 and 1170 cm^-1. Assessment of serum biomarkers of hepatotoxicity indicated significantly altered activities of AST (D*Y: 185.65 ± 8.575 vs Control: 61.9 ± 2.607, D*L: 247.5 ± 5.717 vs Control: 61.9 ± 2.607), ALT (D*Y: 229.8 ± 6.920 vs Control: 70.7 ± 3.109, D*L: 123.75 ± 6.068 vs Control: 70.7 ± 3.109), and ALP (D*Y: 276.4 ± 18.154 vs Control: 320.6 ± 9.829, D*L: 298.5 ± 12.336 vs Control: 320.6 ± 9.829) in IU/L. The analysis of histological alterations showed hepatic sinusoidal dilation with vein congestion and cell infiltration exclusively in D*Y rats along with other histological changes that are common to both test groups, thereby suggesting more pronounced alterations in D*Y rats. Further, LC-MS/MS based label-free quantitation of proteins from liver tissues revealed 74.75% up-regulated, 25.25% down-regulated in D*Y rats and 51.16% up-regulated, 48.84% down-regulated in D*L experiments. The proteomics-identified proteins majorly belonged to metabolism, apoptosis, stress response and redox homeostasis, and detoxification and antioxidant defence that demonstrated the potential damage of rat liver, more pronounced in D*Y rats. Altogether the results are in favor that the administration of lactobacilli somewhat protected the rat hepatic cells against the diclofenac-induced toxicity.</p>","PeriodicalId":8929,"journal":{"name":"Biotechnology Letters","volume":" ","pages":"807-826"},"PeriodicalIF":2.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141562538","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":"Antibiotic-free production of sucrose isomerase in Bacillus subtilis by genome integration.","authors":"Mingyu Li, Ming Xu, Xinrui Bai, Xiang Wan, Meng Zhao, Xianzhen Li, Xiaoyi Chen, Conggang Wang, Fan Yang","doi":"10.1007/s10529-024-03501-3","DOIUrl":"10.1007/s10529-024-03501-3","url":null,"abstract":"<p><p>Sucrose isomerase (SIase) catalyzes the hydrolysis and isomerization of sucrose to form isomaltulose, a valuable functional sugar widely used in the food industry. However, the lack of safe and efficient heterologous expression systems hinders SIase production and application. In this study, we achieved antibiotic-free SIase expression in Bacillus subtilis through genome integration. Using CRISPR/Cas9 system, SIase expression cassettes were integrated into various genomic loci, including amyE and ctc, both individually and in combination, resulting in single-copy and muti-copy integration strains. Engineered strains with a maltose-inducible promoter effectively expressed and secreted SIase. Notably, multi-copy strain exhibited enhanced SIase production, achieving 4.4 U/mL extracellular activity in shake flask cultivations. Furthermore, crude enzyme solution from engineered strain transformed high concentrations sucrose into high yields of isomaltulose, reaching a maximum yield of 94.6%. These findings demonstrate antibiotic-free SIase production in B. subtilis via genome integration, laying the foundation for its industrial production and application.</p>","PeriodicalId":8929,"journal":{"name":"Biotechnology Letters","volume":" ","pages":"781-789"},"PeriodicalIF":2.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141282893","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":"Don't let valuable microbiome data go to waste: combined usage of merging and direct-joining of sequencing reads for low-quality paired-end amplicon data.","authors":"Meganathan P Ramakodi","doi":"10.1007/s10529-024-03509-9","DOIUrl":"10.1007/s10529-024-03509-9","url":null,"abstract":"<p><p>The pernicious nature of low-quality sequencing data warrants improvement in the bioinformatics workflow for profiling microbial diversity. The conventional merging approach, which drops a copious amount of sequencing reads when processing low-quality amplicon data, requires alternative methods. In this study, a computational workflow, a combination of merging and direct-joining where the paired-end reads lacking overlaps are concatenated and pooled with the merged sequences, is proposed to handle the low-quality amplicon data. The proposed computational strategy was compared with two workflows; the merging approach where the paired-end reads are merged, and the direct-joining approach where the reads are concatenated. The results showed that the merging approach generates a significantly low number of amplicon sequences, limits the microbiome inference, and obscures some microbial associations. In comparison to other workflows, the combination of merging and direct-joining strategy reduces the loss of amplicon data, improves the taxonomy classification, and importantly, abates the misleading results associated with the merging approach when analysing the low-quality amplicon data. The mock community analysis also supports the findings. In summary, the researchers are suggested to follow the merging and direct-joining workflow to avoid problems associated with low-quality data while profiling the microbial community structure.</p>","PeriodicalId":8929,"journal":{"name":"Biotechnology Letters","volume":" ","pages":"791-805"},"PeriodicalIF":2.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141544508","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":"A cell-free fluorescence biosensor based on allosteric transcription factor NalC for detection of pentachlorophenol.","authors":"Shuting Chen, Chen Zhao, Xiaodan Kang, Xi Zhang, Bin Xue, Chenyu Li, Shang Wang, Xiaobo Yang, Chao Li, Zhigang Qiu, Jingfeng Wang, Zhiqiang Shen","doi":"10.1007/s10529-024-03511-1","DOIUrl":"10.1007/s10529-024-03511-1","url":null,"abstract":"<p><p>Pentachlorophenol (PCP) was once used as a pesticide, germicide, and preservative due to its stable properties and resistance to degradation. This study aimed to design a biosensor for the quantitative and prompt detection of capable of PCP. A cell-free fluorescence biosensor was developed while employing NalC, an allosteric Transcription Factor responsive to PCP and In Vitro Transcription. By adding a DNA template and PCP and employing Electrophoretic Mobility Shift Assay while monitoring the dynamic fluorescence changes in RNA, this study offers evidence of NalC's potential applicability in sensor systems developed for the specific detection of PCP. The biosensor showed the capability for the quantitative detection of PCP, with a Limit of Detection (LOD) of 0.21 μM. Following the addition of Nucleic Acid Sequence-Based Amplification, the fluorescence intensity of RNA revealed an excellent linear relationship with the concentration of PCP, showing a correlation coefficient (R²) of 0.9595. The final LOD was determined to be 0.002 μM. This study has successfully translated the determination of PCP into a fluorescent RNA output, thereby presenting a novel approach for detecting PCP within environmental settings.</p>","PeriodicalId":8929,"journal":{"name":"Biotechnology Letters","volume":" ","pages":"725-737"},"PeriodicalIF":2.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141625896","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}