Biotechnology Notes最新文献

{"title":"Mevalonate secretion is not mediated by a singular non-essential transporter in Saccharomyces cerevisiae","authors":"Scott A. Wegner ,&nbsp;José L. Avalos","doi":"10.1016/j.biotno.2024.10.001","DOIUrl":"10.1016/j.biotno.2024.10.001","url":null,"abstract":"<div><div>Isoprenoids are highly valued targets for microbial chemical production, allowing the creation of fragrances, biofuels, and pharmaceuticals from renewable carbon feedstocks. To increase isoprenoid production, previous efforts have manipulated pyruvate dehydrogenase (PDH) bypass pathway flux to increase cytosolic acetyl-coA; however, this results in mevalonate secretion and does not necessarily translate into higher isoprenoid production. Identification and disruption of the transporter mediating mevalonate secretion would allow us to determine whether increasing PDH bypass activity in the absence of secretion improves conversion of mevalonate into downstream isoprenoids. Attempted identification of the mevalonate transporter was accomplished using a pooled CRISPR library targeting all nonessential transporters and two different screening methods. Using a high throughput screen, based on growth of a mevalonate auxotrophic <em>Escherichia coli</em> strain, it was found that <em>ZRT3</em> disruption largely abolished accumulation of extracellular mevalonate. However, disruption of <em>ZRT3</em> was found to lower overall mevalonate pathway activity, rather than prevent secretion, indicating a previously unreported interaction between zinc availability and the mevalonate pathway. In a second screen, significant differences in <em>PDR5/15</em> and <em>QDR1/2</em> library representation were found between wild-type and mevalonate secreting <em>Saccharomyces cerevisiae</em> strains. However, no single deletion (or selected pair of double deletions) abolishes mevalonate secretion, indicating that this process appears to be mediated through multiple redundant transporters.</div></div>","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"5 ","pages":"Pages 140-150"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142528967","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":"The potential of copper oxide nanoparticles in nanomedicine: A comprehensive review","authors":"Mahalakshmi Devaraji,&nbsp;Punniyakoti V. Thanikachalam,&nbsp;Karthikeyan Elumalai","doi":"10.1016/j.biotno.2024.06.001","DOIUrl":"https://doi.org/10.1016/j.biotno.2024.06.001","url":null,"abstract":"<div><p>Nanotechnology is a modern scientific discipline that uses nanoparticles of metals like copper, silver, gold, platinum, and zinc for various applications. Copper oxide nanoparticles (CuONPs) are effective in biomedical settings, such as killing bacteria, speeding up reactions, stopping cancer cells, and coating surfaces. These inorganic nanostructures have a longer shelf life than their organic counterparts and are chemically inert and thermally stable. However, commercial synthesis of NPs often involves harmful byproducts and hazardous chemicals. Green synthesis for CuONPs offers numerous benefits, including being clean, harmless, economical, and environmentally friendly. Using naturally occurring organisms like bacteria, yeast, fungi, algae, and plants can make CuONPs more environmentally friendly. CuONPs are expected to be used in nanomedicine due to their potent antimicrobial properties and disinfecting agents for infectious diseases. This comprehensive review looks to evaluate research articles published in the last ten years that investigate the antioxidant, anticancer, antibacterial, wound healing, dental application and catalytic properties of copper nanoparticles generated using biological processes. Utilising the scientific approach of large-scale data analytics. However, their toxic effects on vertebrates and invertebrates raise concerns about their use for diagnostic and therapeutic purposes. Therefore, biocompatibility and non-toxicity are crucial for selecting nanoparticles for clinical research.</p></div>","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"5 ","pages":"Pages 80-99"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665906924000102/pdfft?md5=1bd90f034c802d80d953cb65ac2eab2a&pid=1-s2.0-S2665906924000102-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141292369","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":"aXonica: A support package for MRI based Neuroimaging","authors":"Bilal Wajid ,&nbsp;Momina Jamil ,&nbsp;Fahim Gohar Awan ,&nbsp;Faria Anwar ,&nbsp;Ali Anwar","doi":"10.1016/j.biotno.2024.08.001","DOIUrl":"10.1016/j.biotno.2024.08.001","url":null,"abstract":"<div><p>Magnetic Resonance Imaging (MRI) assists in studying the nervous system. MRI scans undergo significant processing before presenting the final images to medical practitioners. These processes are executed with ease due to excellent software pipelines. However, establishing software workstations is non-trivial and requires researchers in life sciences to be comfortable in downloading, installing, and scripting software that is non-user-friendly and may lack basic GUI. As researchers struggle with these skills, there is a dire need to develop software packages that can automatically install software pipelines speeding up building software workstations and laboratories. Previous solutions include NeuroDebian, BIDS Apps, Flywheel, QMENTA, Boutiques, Brainlife and Neurodesk. Overall, all these solutions complement each other. NeuroDebian covers neuroscience and has a wider scope, providing only 51 tools for MRI. Whereas, BIDS Apps is committed to the BIDS format, covering only 45 software related to MRI. Boutiques is more flexible, facilitating its pipelines to be easily installed as separate containers, validated, published, and executed. Whereas, both Flywheel and Qmenta are propriety, leaving four for users looking for ‘free for use’ tools, i.e., NeuroDebian, Brainlife, Neurodesk, and BIDS Apps. This paper presents an extensive survey of 317 tools published in MRI-based neuroimaging in the last ten years, along with ‘aXonica,’ an MRI-based neuroimaging support package that is unbiased towards any formatting standards and provides 130 applications, more than that of NeuroDebian (51), BIDS App (45), Flywheel (70), and Neurodesk (85). Using a technology stack that employs GUI as the front-end and shell scripted back-end, aXonica provides (i) 130 tools that span the entire MRI-based neuroimaging analysis, and allow the user to (ii) select the software of their choice, (iii) automatically resolve individual dependencies and (iv) installs them. Hence, aXonica can serve as an important resource for researchers and teachers working in the field of MRI-based Neuroimaging to (a) develop software workstations, and/or (b) install newer tools in their existing workstations.</p></div>","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"5 ","pages":"Pages 120-136"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665906924000126/pdfft?md5=586029896db2ec4af16780650f840978&pid=1-s2.0-S2665906924000126-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142149205","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":"Antibiotic susceptibility and virulence factors of bacterial species among cancer patients","authors":"Gamal M. El-Sherbiny ,&nbsp;Eman E. Farghal ,&nbsp;Mohamed K. Lila ,&nbsp;Yousseria M. Shetaia ,&nbsp;S.S. Mohamed ,&nbsp;Marwa MF. Elswify","doi":"10.1016/j.biotno.2024.02.002","DOIUrl":"10.1016/j.biotno.2024.02.002","url":null,"abstract":"<div><p>Antibiotic resistance is one of the most significant challenges of the 20-s century, and the misuse of antibiotics is a driver of antimicrobial resistance. This study aimed to assess the prevalence of multidrug resistance, and detection of its produce virulence factors, including extended-spectrum β-lactamases (ESβLs), biofilm, and siderophores produced by bacterial species isolated from cancer patients. One hundred and seventy-five Gram-negative bacterial isolates were isolated from different samples collected from cancer patients admitted to the National Cancer Institute (NCI), Cairo, Egypt, and processed by standard microbiological methods. One hundred and forty-three bacterial isolates were recovered from adult patients, and 32 were recovered from children. <em>Escherichia coli</em> showed the highest frequency (36%), followed by <em>Klebsiella pneumonia</em> (30.85%), <em>Acinetobacter baummannii</em> (14.28%), and <em>Pseudomonas</em> sp. (9.14%). Antibiotic profiles revealed that bacterial isolates are highly resistant to the most commonly available antibiotics. Amikacin and gentamicin were the most effective antibiotics against isolated Gram-negative bacteria. Moreover, the vast majority of bacterial stains produce virulence factors, including EsβLs, biofilm, and siderophores. <em>E. coli</em> isolates produced ESβLs with rates of 25.28%, <em>Klebsiella pneumonia</em> (11.0%), and <em>Pseudomonas</em> sp. (25.0%). Among these collected bacterial isolates, 132 (75.4%) have the ability to form a biofilm to different degrees. Also, the majority of the bacteria isolates generated siderophores, with 133 (75.94%). This study revealed that a significant distribution of multidrug-resistant pathogenic bacteria may increase the burden on healthcare to prevent infections in cancer patients.</p></div>","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"5 ","pages":"Pages 27-32"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665906924000059/pdfft?md5=a4cbb8c1c8e233851aa0e7c0fcc49313&pid=1-s2.0-S2665906924000059-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139967021","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":"A comparative exploration of mRNA capping enzymes","authors":"Yiming Wang ,&nbsp;Xiaoxue Wang ,&nbsp;Wenchao Li ,&nbsp;Xinjie Chen ,&nbsp;Yuan Lu","doi":"10.1016/j.biotno.2024.11.005","DOIUrl":"10.1016/j.biotno.2024.11.005","url":null,"abstract":"<div><div>With the wide application of messenger RNA (mRNA) technology in medicine and vaccine fields, higher requirements are put forward for mRNA expression efficiency <em>in vivo</em>. Since the 5′ cap structure can spatially protect mRNA from exonuclease degradation and enhance the initiation of translation reactions, <em>in vitro</em> mRNA caps are a promising option to improve the efficiency of mRNA expression <em>in vivo</em>. In order to obtain more efficient mRNA capping enzymes, seven mRNA capping enzymes from different viral sources were explored in this study. Eukaryotic and prokaryotic cells were used for the heterologous expression of the cap enzymes, and <em>Escherichia coli</em> was identified as the most suitable host cell for heterologous expression. In addition, in order to improve the solubility of the capping enzyme, four kinds of soluble labels were screened, among which maltose-binding protein had the best effect and the widest applicability. The mRNA was then transfected into the human cells, and the highest transfection efficiency was achieved using the bluetongue virus capping enzyme. Its effect was 38 % higher than that of the previously widely used vaccinia virus capping enzyme. This work will promote the development of mRNA technology and expand its application space.</div></div>","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"5 ","pages":"Pages 165-172"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142704172","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":"Screening, characterization, and production of Bacillus cereus (S55) bioflocculant isolated from soil for application in wastewater treatment","authors":"Karthikeyan Harinisri ,&nbsp;Ragothaman Prathiviraj ,&nbsp;Balasubramanian Thamarai Selvi","doi":"10.1016/j.biotno.2024.11.003","DOIUrl":"10.1016/j.biotno.2024.11.003","url":null,"abstract":"<div><div>This research evaluated a bacterial strain, <em>Bacillus cereus</em> (S55), isolated from the soil for its bioflocculant production capabilities. The strain was identified through morphological and 16s rRNA gene sequencing. The optimization of culture conditions, using One-factor-at-a-time method, significantly enhanced bioflocculant production with glucose and urea. FTIR analysis showed the presence of hydroxyl, amine and carboxylate functional groups, with polysaccharides as predominant components. Scanning electron microscopy and X-ray diffraction confirmed the crystalline nature of the bioflocculant. The strain studied showed potential in treating household wastewater and was effective at removing dyes, suggesting alternatives for wastewater management.</div></div>","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"5 ","pages":"Pages 151-164"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142658470","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":"Organ-on-chip technology: Opportunities and challenges","authors":"Santosh Kumar Srivastava ,&nbsp;Guo Wei Foo ,&nbsp;Nikhil Aggarwal ,&nbsp;Matthew Wook Chang","doi":"10.1016/j.biotno.2024.01.001","DOIUrl":"10.1016/j.biotno.2024.01.001","url":null,"abstract":"<div><p>Organ-on-chip (OOC) technology is an innovative approach that reproduces human organ structures and functions on microfluidic platforms, offering detailed insights into intricate physiological processes. This technology provides unique advantages over conventional in vitro and in vivo models and thus has the potential to become the new standard for biomedical research and drug screening. In this mini-review, we compare OOCs with conventional models, highlighting their differences, and present several applications of OOCs in biomedical research. Additionally, we highlight advancements in OOC technology, particularly in developing multiorgan systems, and discuss the challenges and future directions of this field.</p></div>","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"5 ","pages":"Pages 8-12"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665906924000023/pdfft?md5=3d6c8e49497bcf18217860d3c12546f2&pid=1-s2.0-S2665906924000023-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139392265","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":"Understanding virus retention mechanisms on protein a chromatography based on using different wash buffers – Evaluating the possibility for a generic wash buffer toolbox to improve virus clearance capacity","authors":"Sandra Krause ,&nbsp;Florian Capito ,&nbsp;Verena Oeinck ,&nbsp;Hendrik Flato ,&nbsp;Holger Hoffmann ,&nbsp;Ozan Ötes ,&nbsp;Annette Berg","doi":"10.1016/j.biotno.2024.03.001","DOIUrl":"https://doi.org/10.1016/j.biotno.2024.03.001","url":null,"abstract":"<div><p>During manufacturing of mammalian-cell derived monoclonal antibodies (mAbs) virus clearance capacity of the downstream process has to be demonstrated. The protein A chromatography step typically achieves less than 4 log₁₀ and is not considered as a major contributing step. Having been successfully applied to host cell protein removal before, we used different wash buffers for three mAbs with two model viruses (Minute virus of mice and Murine leukemia virus) in series as well as separately to further understand major contributing interactions for virus retention and potentially design a generic toolbox of stringent wash buffers to be applied to various mAbs. Results indicate a major relevance of hydrophobic interaction for Murine leukemia virus (xMuLV) and mAb A, based on improved clearance for buffers additionally containing increased levels of hydrophobic compounds. This effect was less pronounced for Minute virus of mice (MVM), whereby hydrogen-bonds were expected to play a stronger role for this model virus. Additionally, electrostatic interactions presumably are more relevant for MVM retention compared to xMuLV under the conditions evaluated. A generic mAb and virus-independent stringent wash buffer toolbox could not be identified. However, based on our results a customized mAb and virus wash buffer design with improved virus clearance is possible, with here demonstrated log reduction increase by 1.3 log₁₀ for MVM and 2.2 log₁₀ for xMuLV for the protein A step compared to equilibration buffer alone.</p></div>","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"5 ","pages":"Pages 50-57"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665906924000060/pdfft?md5=d90d78b9590b013af6078b5615adb6ad&pid=1-s2.0-S2665906924000060-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140348246","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":"Incorporating omics-based tools into endophytic fungal research","authors":"Vinita Verma ,&nbsp;Alok Srivastava ,&nbsp;Sanjay Kumar Garg ,&nbsp;Vijay Pal Singh ,&nbsp;Pankaj Kumar Arora","doi":"10.1016/j.biotno.2023.12.006","DOIUrl":"https://doi.org/10.1016/j.biotno.2023.12.006","url":null,"abstract":"<div><p>Fungal endophytes are valuable sources of bioactive compounds with diverse applications. The exploration of these compounds not only contributes to our understanding of ecological interactions but also holds promise for the development of novel products with agricultural, medicinal, and industrial significance. Continued exploration of fungal endophyte diversity and understanding the ecological roles of bioactive compounds present opportunities for new discoveries and applications. Omics techniques, which include genomics, transcriptomics, proteomics, and metabolomics, contribute to the discovery of novel bioactive compounds produced by fungal endophytes with their potential applications. The omics techniques play a critical role in unraveling the complex interactions between fungal endophytes and their host plants, providing valuable insights into the molecular mechanisms and potential applications of these relationships. This review provides an overview of how omics techniques contribute to the study of fungal endophytes.</p></div>","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"5 ","pages":"Pages 1-7"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665906923000259/pdfft?md5=222a86c032e0d932ffc20dd4a771b7fe&pid=1-s2.0-S2665906923000259-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139108011","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":"The role of brain-derived neurotrophic factor and its recombinant pro-isoforms in depressive disorder: Open questions","authors":"Éllen F. Rodrigues ,&nbsp;Ana L. Fachin ,&nbsp;Mozart Marins ,&nbsp;Felipe Britto Letieri ,&nbsp;Rodrigo G. Stabeli ,&nbsp;Renê O. Beleboni","doi":"10.1016/j.biotno.2024.09.001","DOIUrl":"10.1016/j.biotno.2024.09.001","url":null,"abstract":"","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"5 ","pages":"Pages 137-139"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2665906924000138/pdfft?md5=861ce1318e9bec03122f8b124bb9ead0&pid=1-s2.0-S2665906924000138-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142168266","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}