Araya Jivapetthai , Wanatchaporn Arunmanee , Natapol Pornputtapong
{"title":"Quality by design for transient RBD-Fc fusion protein production in Chinese hamster ovary cells","authors":"Araya Jivapetthai , Wanatchaporn Arunmanee , Natapol Pornputtapong","doi":"10.1016/j.btre.2025.e00882","DOIUrl":"10.1016/j.btre.2025.e00882","url":null,"abstract":"<div><div>Quality by design (QbD) is applied to the upstream process to maximize the RBD-Fc fusion protein production in CHO cells. The three factors (culture duration, temperature, and polyethyleneimine to plasmid DNA (PEI-Max/pDNA) ratio) were identified as critical process attributes based on risk analysis (FMEA) and further optimized by response surface to maximize the protein yields. Using a Box-Behnken design, the optimal conditions for RBD-Fc production were determined to be a culture duration of 5 days, a culture temperature of 34.4 °C, and a PEI-Max/pDNA ratio of 4.2:1 (w/w) with a predictive value of 48 mg/L (desirability of 92.8 %). The PEI-Max/pDNA ratio and its interaction with culture duration to express the highest yield (47.78 ± 2.30 mg/l). In addition, the purified CHO-produced RBD-Fc fusion protein was highly pure and strongly bound to its receptor, ACE2. Our finding demonstrated that the QBD tools can identify the critical parameters to facilitate scaling-up production.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"45 ","pages":"Article e00882"},"PeriodicalIF":0.0,"publicationDate":"2025-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143419172","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}
Abdul Jalil Shah , Mohammad Younis Dar , Mohd Adnan , Tanmaykumar Varma , Dhairiya Agarwal , Prabha Garg , Reyaz Hassan Mir , Rampratap Meena , Mubashir Hussain Masoodi
{"title":"Integration of phytochemical profiling and computational approaches to evaluate the neuroprotective potential of Nardostachys jatamansi in Alzheimer's disease","authors":"Abdul Jalil Shah , Mohammad Younis Dar , Mohd Adnan , Tanmaykumar Varma , Dhairiya Agarwal , Prabha Garg , Reyaz Hassan Mir , Rampratap Meena , Mubashir Hussain Masoodi","doi":"10.1016/j.btre.2025.e00881","DOIUrl":"10.1016/j.btre.2025.e00881","url":null,"abstract":"<div><div>Despite broad spectrum utility of <em>Nardostachys jatamansi</em> (D. Don) DC, little is known about the molecular processes that underlie its anti-Alzheimer action. To investigate the molecular targets and therapeutic potential of <em>N. jatamansi</em> for Alzheimer's disease (AD), we used Gas Chromatography-Mass Spectrometry (GC-MS), ADMET analysis, network pharmacology, differential gene expression analysis, molecular docking, and molecular dynamics (MD) simulations. The STITCH database was used for network creation and protein-protein interaction analysis, while Cytoscape was used for network visualization and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and Gene Ontology (GO) for term enrichment. Additionally, to investigate the intermolecular interactions between the active chemicals and target proteins, molecular docking experiments were conducted using the Blind docking on the Achilles server. The stability of the PS1 gene complex with Spirojatamol, was further evaluated using MD simulations. With Spirojatamol showing the highest binding energy scores against PS1 (−6.9 kcal/mol), molecular docking confirmed the activity of this metabolite against AD targets PS1 and Spirojatamol formed a stable complex at 100 nanoseconds, according to additional investigation using MD simulations. Significant ligand-protein interactions were verified by binding free energy calculations using the MM/GBSA technique. The PS1-Spirojatamol complex had a binding energy of ΔG: −36.95 ± 5.00 kcal/mol. By focusing on several genes and pathways, involved in AD, this work reveals the molecular underpinnings behind <em>N. jatamansi</em> possible use in the treatment of AD.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"45 ","pages":"Article e00881"},"PeriodicalIF":0.0,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143419171","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":"Salinity induced changes in esterase, peroxidase and alcohol dehydrogenase isozymes and leaf soluble proteins in salinity susceptible and salinity tolerant sugarcane genotypes","authors":"Manisha Rameshrao Patil , A.A. Kale , Ajay Kumar Singh , Priyanka Rameshrao Patil , Shaheen Badshah Inamdar , R.D. Satbhai","doi":"10.1016/j.btre.2025.e00880","DOIUrl":"10.1016/j.btre.2025.e00880","url":null,"abstract":"<div><div>The salinity susceptible CoC-671 and salinity tolerant sugarcane genotype CoM-265 were evaluated for Peroxidase (POX), Esterase (EST) and Alcohol Dehydrogenase (ADH) isozymes and soluble protein profiling by SDS and native-PAGE at salinity levels 0.41 dSm<sup>-1</sup>, 2.31 dSm<sup>-1</sup>, 4.21 dSm<sup>-1</sup>, and 8.01 dSm<sup>-1</sup> maintained by NaCl solution. The plant height, number of leaves and seedling diameter got reduced in salinity susceptible sugarcane genotype CoC-671 as well as salinity tolerant sugarcane genotype CoM-265 with increase in salinity levels. However, reduction in plant height, number of leaves and seedling diameter was less in salinity tolerant sugarcane genotype CoM-265 as compared to salinity susceptible sugarcane genotype CoC-671. The POX isozyme profiling revealed that salinity susceptible CoC-671 and salinity tolerant sugarcane genotype CoM-265 had variation in soluble protein band intensity at different salinity levels with relative mobility (Rm) 0.137. The present study could be useful for genetic variability analysis in sugarcane genotypes differing in salinity stress tolerance capability.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"45 ","pages":"Article e00880"},"PeriodicalIF":0.0,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143429064","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":"Identification and purification of a novel bacteriophage T7 endonuclease from the Kogelberg Biosphere Reserve (KBR) biodiversity hotspot","authors":"Priyen Pillay , Maabo Moralo , Sibongile Mtimka , Taola Shai , Kirsty Botha , Lusisizwe Kwezi , Tsepo L. Tsekoa","doi":"10.1016/j.btre.2025.e00877","DOIUrl":"10.1016/j.btre.2025.e00877","url":null,"abstract":"<div><div>The four-way (Holliday) DNA junction is a key intermediate in homologous recombination, a ubiquitous process that is important in DNA repair and generation of genetic diversity. The final stages of recombination require resolution of the junction into nicked-duplex species by the action of a junction-resolving enzyme. The enzymes involved are nucleases that are highly selective for the structure of branched DNA. Here we present the isolation, expression and purification of a novel T7 endonuclease from the Kogelberg Biosphere Reserve (KBR), which possesses junction resolving capabilities. An initial approach was employed where the process was scaled up to 3 L with IPTG concentration of 0.1 mM at 30 °C and purified via immobilised metal affinity chromatography (IMAC). Expression titres of 20 ± 0.003 µg.L<sup>-1</sup> culture were achieved with the amount of KBR-T7 endonuclease required per reaction ranging from as low as 10 to 100 nanograms. The solubility of the enzyme was relatively poor; however, enzyme activity was not affected. A derivative for improved solubility and efficacy was then designed from this original wild-type version, MBP-KBR-T7 and was expressed under similar conditions at 20 °C yielding 1.63 ± 0.154 mg.L<sup>-1</sup> of formulated enzyme. This novel high value enzyme derivative is a valuable asset within the molecular reagent space as a tool for confirming both <em>in vivo</em> and <em>in vitro</em> genome editing; therefore, a means to produce it recombinantly in a scalable and technoeconomicaly viable process is highly desirable.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"45 ","pages":"Article e00877"},"PeriodicalIF":0.0,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143103879","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}
Thomas Loan , Avinash Karpe , Saeid Babaei , Stuart Denman , Chunghong Chen , Matthias Joust , Kristy Lam , Dawar Hussain , Sapna Pillai Vibhakaran , Matthew Callaghan , Abed Chaudhury , Karen Paco , Nigel Tomkins , Tristan Yang , Stephanie Payne , Michael Ayliffe , Ming Luo
{"title":"Biosynthesis of bromoform by Curvularia fungi provides a natural pathway to mitigate enteric methane emissions from ruminants","authors":"Thomas Loan , Avinash Karpe , Saeid Babaei , Stuart Denman , Chunghong Chen , Matthias Joust , Kristy Lam , Dawar Hussain , Sapna Pillai Vibhakaran , Matthew Callaghan , Abed Chaudhury , Karen Paco , Nigel Tomkins , Tristan Yang , Stephanie Payne , Michael Ayliffe , Ming Luo","doi":"10.1016/j.btre.2025.e00876","DOIUrl":"10.1016/j.btre.2025.e00876","url":null,"abstract":"<div><div>The ruminant livestock industry is the largest agricultural emissions source of anthropogenic greenhouse gases, primarily from enteric methane. Several technologies, both natural and synthetic are being investigated to mitigate enteric methane emissions. Macroalgae derived feed ingredients that contain bromoform, a recognised inhibitor of methanogenesis, are an effective natural approach for methane mitigation. However, producing sufficient biomass economically to satisfy the livestock industry at a global scale is challenging. Here we demonstrate that a <em>Curvularia</em> soil fungi isolate can be cultured to produce bromoform and subsequently inhibit methanogenesis in pure cultures of <em>Methanobrevibacter smithii</em> and in mixed cultures of ovine rumen fluid. This highly culturable fungal species produces no known toxins and creates an exciting new, scalable and natural alternative for reducing ruminant livestock emissions.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"45 ","pages":"Article e00876"},"PeriodicalIF":0.0,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143103878","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":"Fungal – assisted microalgae flocculation and simultaneous lignocellulolytic enzyme production in wastewater treatment systems","authors":"Anna Civzele, Linda Mezule","doi":"10.1016/j.btre.2025.e00875","DOIUrl":"10.1016/j.btre.2025.e00875","url":null,"abstract":"<div><div>The study investigates the application of white rot fungi for reactor–scale microalgae harvesting and explores the mechanisms underlying the algal–fungal interactions and their impact on biomass composition. Enzymatic analysis and microscopy revealed that the formation of algal-fungal complexes and successful harvesting are coupled with fungal cellulose-degrading enzyme production and hydrolytic processes of microalgae cells. Fluorescence intensity decreased by over 80 % in cells stained with Calcofluor-white after interaction with white rot fungi, indicating the reduction in cellulose content in microalgal cells caused by fungal enzymatic activity. These enzymes also caused significant cell damage and more than 50 % decrease in microalgae cell size. The presence of cellulolytic enzymes broadens the potential application of the resulting biomass in various biotechnological applications. Moreover, reactor-scale bioflocculation resulted in over 95 % <em>T. obliquus</em> and almost 85 % <em>C. vulgaris</em> harvesting efficiency from secondary wastewater within less than 24 h, demonstrating the method's scalability and industrial applicability.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"45 ","pages":"Article e00875"},"PeriodicalIF":0.0,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143103880","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":"Cobalt phosphide-loaded biochar synthesis using phosphate-accumulating yeast and its application as an electrocatalyst","authors":"Yoshihiro Ojima , Riho Akiyoshi , Itto Tokiwa , Takashi Nakazono , Yusuke Yamada , Masayuki Azuma","doi":"10.1016/j.btre.2025.e00874","DOIUrl":"10.1016/j.btre.2025.e00874","url":null,"abstract":"<div><div>A phosphorus (P)-accumulating mutant strain of <em>Saccharomyces cerevisiae</em> is used as a precursor for transition metal phosphides (TMPs) biochar. Tetrahydrofuran treatment of the P-accumulating yeast coupled with pyrolysis resulted in the formation of CoP-loaded biochar (CoP@P-yeast) unlike previously reported Co<sub>2</sub>P-loaded biochar using dry baker's yeast. The CoP@P-yeast exhibited the electrocatalytic activity for the hydrogen evolution with an overpotential of −192 mV at 10 mA cm<sup>−2</sup>. Furthermore, the CoP@P-yeast showed the highest ammonia production rate of 33 mg-NH<sub>3</sub> h<sup>−1</sup> mg-catalyst<sup>−1</sup> in nitrate reduction reaction, as well as much higher than that with platinum on graphitized carbon. Scanning electron microscopy and transmission electron microscopy observations revealed that relatively large TMP crystals mainly located at the biochar surface, which may be beneficial to avoid catalytic deterioration during the nitrate reduction reaction. This study demonstrates that P-accumulating mutant strain of yeast is a suitable precursor to improve the activity of the resulting TMP biochar.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"45 ","pages":"Article e00874"},"PeriodicalIF":0.0,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11787416/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143081538","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":"Valorization of agro-industrial waste through solid-state fermentation: Mini review","authors":"Mohammad Perwez , Sameer Al Asheh","doi":"10.1016/j.btre.2024.e00873","DOIUrl":"10.1016/j.btre.2024.e00873","url":null,"abstract":"<div><div>Agriculture and industrial waste are produced in large volumes every year worldwide, causing serious concerns about their disposal. These wastes have high organic content, which microorganisms can easily assimilate into relevant value-added products. Valorization of agro-industrial waste is required for sustainable development. Solid state fermentation is an excellent method of utilizing waste for circular bioeconomy. Exploitation of agro-industrial waste as a substrate utilizing microorganisms for solid state fermentation provides beneficial products for use in industries and other fields. The use of waste reduces the cost of production of value-added products. This method is an environmentally friendly, economical and feasible approach for waste management. This review discusses the factors affecting the production of value-added products through solid state fermentation. It also discusses the valuable products from solid state fermentation technology, such as antibiotics, enzymes, organic acids, bioremediation, biosurfactants and biofertilizers. Challenges and future prospects are also presented.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"45 ","pages":"Article e00873"},"PeriodicalIF":0.0,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11780145/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143068466","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}
Ihtisham Ul Haq , Kashif Rahim , Sajida Maryam , Najeeba Parre Paker
{"title":"Bacteriophage-based biosensors technology: Materials, fabrications, efficiencies and shortcomings","authors":"Ihtisham Ul Haq , Kashif Rahim , Sajida Maryam , Najeeba Parre Paker","doi":"10.1016/j.btre.2024.e00872","DOIUrl":"10.1016/j.btre.2024.e00872","url":null,"abstract":"<div><div>Ongoing research in biosensor technologies has led to advanced functional materials for healthcare diagnostics, and bacteriophages (phages), demonstrating exceptional utility due to their high specificity, accuracy, rapid, label-free, and wireless detection capabilities with minimal false-positive results. Phage-based-pathogen-detecting biosensors (PBPDBs) include surface plasmon resonance (SPR) biosensors, magnetoelastic (ME), electrochemical, and quartz crystal microbalance (QCM) biosensors. Commonly used substrates for PBPDBs are gold, silicon, glass, carbon-based materials, magnetic particles, and quantum dots. These substrates are chemically and physically modified to optimize phage orientation on sensor surfaces, enhancing bacterial capture. To address typical stability and issues encountered in traditional biosensor applications, phage particles and genetically modified phages are utilized to improve biosensor stability and increase detection efficacy while reducing assay time. Genetic modification in phages facilitated by CRISPR/Cas9 enables the tailoring of phages to target specific bacterial strains. This approach helps overcome the inherent specificity of phages and enables the detection of multiple pathogens in a single assay. Multiple pathogens can be detected through a single phage-based assay. This manuscript elucidates the fabrication methodologies and detection efficiencies of PBPDBs providing valuable insights into the development of practical, precise, and efficient biosensors for pathogen detection.</div></div><div><h3>Summary</h3><div>PBPDBs are emerging diagnostic tools for the detection of bacterial pathogens.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"45 ","pages":"Article e00872"},"PeriodicalIF":0.0,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11732128/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142984956","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}
Doha H. Aboubaker , Nermeen A. Shaffie , Mona F. Shabana , Ahmed Abd Elghafour , Bassant M.M. Ibrahim
{"title":"Protective role of savory essential oil on vital organs in rats against deleterious effects induced by lead acetate","authors":"Doha H. Aboubaker , Nermeen A. Shaffie , Mona F. Shabana , Ahmed Abd Elghafour , Bassant M.M. Ibrahim","doi":"10.1016/j.btre.2024.e00871","DOIUrl":"10.1016/j.btre.2024.e00871","url":null,"abstract":"<div><div>The damaging effects of heavy metal exposure on vital organs like the heart, liver, kidneys, and brain can be lowered by natural compounds' anti-inflammatory and anti-oxidant capacity. In the current investigation, the protective potential of savory(<em>Saturejahortensis</em>)essential oil (EO) against lead acetate-induced multi-organ damage in rats was evaluated. Thirty female Wister Albino rats were divided into the following groups: normal, positive control given lead acetate without concomitant treatment, reference given ethylene-diamine-tetra-acetic acid and groups treated with savory EO (0.5 and 1 ml/rat), treatments were administered concomitantly with lead acetate for ten successive days. Electrocardiogram (ECG), open field, and rota-rod tests for evaluation of behaviour, as well as TNF-α, R-GSH & MDA were measured in brain and liver homogenates respectively, CRP, liver, kidney, and heart function tests, were measured in serum. Histopathology of vital organs was conducted at the end of the experiment.A high dose of savory EO, significantly improved the cardiac electrophysiology, psychological state, and locomotor activity of rats; moreover, it lowered inflammatory, oxidative biomarkers, liver, kidney, and cardiac function tests of the rats. Savory EO protects vital organs against heavy metal damage with the superiority of the high dose.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"45 ","pages":"Article e00871"},"PeriodicalIF":0.0,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11732139/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142985051","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}