Biotechnology Notes最新文献

{"title":"Straightforward MALDI-TOF MS based screening approach for selection of recombinant protein-expressing E. coli","authors":"I.N. Kravtsov ,&nbsp;A.I. Solovyev ,&nbsp;E.A. Potemkina ,&nbsp;A.V. Kartashova ,&nbsp;M.A. Dmitrieva ,&nbsp;K.V. Danilova ,&nbsp;I.L. Tutykhina ,&nbsp;N.B. Polyakov ,&nbsp;V.D. Desinov ,&nbsp;D.A. Egorova ,&nbsp;A.L. Gintsburg","doi":"10.1016/j.biotno.2025.02.004","DOIUrl":"10.1016/j.biotno.2025.02.004","url":null,"abstract":"<div><div>Recombinant protein production is a milestone of modern biotechnology, drug development and scientific research. When obtaining recombinant protein producers, differences in expression levels among clones necessitate screening. Traditional widely used methods include protein electrophoresis and western blot hybridization. This protocol provides high-throughput advantages by eliminating time-consuming steps inherent to traditional methods, such as cell lysis, protein extraction, purification, antibody-based detection, and gel-based analysis. MALDI-TOF MS represents a simple, rapid and cost-effective method for bacterial species identification through protein fingerprint signature in clinical diagnostics, but not practically integrated into biotechnological workflow. This study proposes a fast and easy method for screening <em>E. coli</em> clones producing recombinant proteins with MALDI-TOF MS. The proposed method demonstrated efficiency in screening of <em>E. coli</em> producing several recombinant proteins with different properties: sfGFP; bacterial DNA binding proteins IHF<em>α</em>, IHF<em>β</em>, HU; bacteriophage protein GP46 and camelid VHH antibody fragments.</div></div>","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"6 ","pages":"Pages 100-105"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143551780","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":"Agroinfiltration-mediated transient assay for rapid evaluation of constructs in pigeonpea","authors":"Kalenahalli Yogendra,&nbsp;Harika Gadeela,&nbsp;Koppula Nithya Sree,&nbsp;Wricha Tyagi","doi":"10.1016/j.biotno.2025.02.005","DOIUrl":"10.1016/j.biotno.2025.02.005","url":null,"abstract":"<div><div>The process of generating stable transformants is time-consuming, labor-intensive, and genotype-dependent. In contrast, transient gene expression techniques, such as agroinfiltration, offer a rapid assessment of gene function and expression. Agroinfiltration, widely employed for studying gene function, has been extensively applied in leaf tissues of <em>Nicotiana benthamiana</em> and various other plant species. Despite its broad utility in various plants, to our knowledge, no prior investigation has been reported in pigeonpea. In this study, we developed an agroinfiltration method for transiently expressing a green fluorescent protein (<em>mGFP5</em>) reporter gene in four pigeonpea genotypes using syringe infiltration at the seedling stage under greenhouse conditions. The expression of the reporter gene <em>mGFP5</em> was assessed at 72-, 96-, and 120 h post-infiltration (hpi). Additionally, we assessed the effect of morphogenic genes, specifically <em>growth-regulating factor 4</em> (<em>GRF4</em>) and <em>GRF-interacting factor 1</em> (<em>GIF1</em>), from both rice and pigeonpea on the expression of <em>mGFP5</em> in four pigeonpea genotypes. Our findings demonstrate that <em>OsGRF4-GIF1</em> led to enhanced <em>mGFP5</em> expression compared to <em>CcGRF4-GIF1</em> in four diverse pigeonpea genotypes. Fluorescence could be detected till 120 hpi. Furthermore, PCR, RT-PCR, and fluorescence quantification confirmed the presence and expression of <em>mGFP5</em> at 72 hpi. Our results highlight the efficacy of agroinfiltration in quickly evaluating candidate genes in four genetically diverse pigeonpea genotypes, thereby reducing the time required for the initial assessment of constructs suitable for diverse molecular biology analyses.</div></div>","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"6 ","pages":"Pages 117-125"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143580157","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":"Cell-free protein synthesis platforms for accelerating drug discovery","authors":"Filippo Caschera","doi":"10.1016/j.biotno.2025.02.001","DOIUrl":"10.1016/j.biotno.2025.02.001","url":null,"abstract":"<div><div>Cell-free protein synthesis is a platform for streamlined production of macromolecules. Recently, several proteins with pharmaceutical relevance were synthesised and characterised. Off-the-shelf reagents and parallelised experimentation have enabled the exploration of many different conditions for <em>in vitro</em> protein synthesis and engineering. Herein is described how machine learning algorithms were applied for protein yield maximisation as well as for protein engineering and <em>de novo</em> design. Cell-free protein synthesis provides the biotechnological platform to unlock the power and benefit of AI/ML for drug discovery and improve human health.</div></div>","PeriodicalId":100186,"journal":{"name":"Biotechnology Notes","volume":"6 ","pages":"Pages 126-132"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143579849","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":"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}