Rhosener Bhea L Koh, Jose Planta, Richard I Encarnacion, Jasca Gayle G Española, Vermando M Aquino, Leny C Galvez
{"title":"Efficient RNA extraction method for acquiring high-quality RNA from various tissues of the fiber crop abaca, <i>Musa textilis</i> Née.","authors":"Rhosener Bhea L Koh, Jose Planta, Richard I Encarnacion, Jasca Gayle G Española, Vermando M Aquino, Leny C Galvez","doi":"10.1080/10826068.2024.2440421","DOIUrl":"https://doi.org/10.1080/10826068.2024.2440421","url":null,"abstract":"<p><p>Isolation of high-quality RNA from abaca is very challenging due to the presence of polyphenols, polysaccharides, and its high fiber content. In this study, we compared six extraction methods across three tissue types and different developmental stages (<i>in-vitro</i>-grown young versus field-grown mature tissue). The Invitrogen PureLink RNA kit proved to be the most efficient in extracting RNA from young abaca tissues (leaves, pseudostem, and corm). The quality of RNA extracted from young tissues was further assessed by RNA-seq applications, with raw sequencing reads mapping back to the <i>M. textilis</i> reference genome at rates of 86.0%-90.4%. The SDS-TRIzol-method modified with an added on-column DNAse I treatment was used to extract RNA from mature tissues (leaves, midrib, and pseudostem). RNA isolated from five <i>M. textilis</i> cultivars and across three mature tissue types showed RNA yield per 100 mg of fresh weight ranges from 0.57 to 10.94 µg and RNA integrity number (RIN) scores of more than 7.0 for all tissue types. Our improved SDS-Trizol method for RNA extraction described here is simple and yields good quality RNAs from mature abaca tissues while the PureLink RNA kit is suitable for extracting RNA from young abaca samples amenable to RT-qPCR and next-generation sequencing studies.</p>","PeriodicalId":20401,"journal":{"name":"Preparative Biochemistry & Biotechnology","volume":" ","pages":"1-12"},"PeriodicalIF":2.0,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142838774","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":"Harnessing algal biomass for sustainable energy: cultivation, strain improvement, and biofuel production.","authors":"Indira Mikkili, Bala Venkata Sai Teja Gaddirala, Sudarsini Borugadda, Syam Babu Davuluri","doi":"10.1080/10826068.2024.2434879","DOIUrl":"https://doi.org/10.1080/10826068.2024.2434879","url":null,"abstract":"<p><p>The world faces pressing environmental challenges, including greenhouse gas emissions, global warming, climate change, and rising sea levels. Alongside, these issues, the depletion of fossil fuels has intensified the search for alternative energy sources. Algal biomass presents a promising long-term solution to these global problems. The quest for sustainable energy has driven significant research into algal biofuels as a viable alternative to fossil fuels. Algae offers several advantages as a feedstock for biofuel production, including high biomass yield, rapid growth rates, cost-effective cultivation, carbon dioxide fixation capabilities, and the potential to grow on non-arable land using non-potable water. This manuscript provides an overview of algal biomass cultivation using renewable feedstocks, identifies potential algal strains for biofuel production, and explores bioengineering advancements in algae. Additionally, strain improvement strategies to enhance biofuel yields are discussed. The review also addresses large-scale algal biomass cultivation for biofuel production, assesses its commercial viability, examines challenges faced by the biofuel industry, and outlines prospects for biofuel production using highly potent algal strains. By overcoming and addressing these challenges, algal biofuels have the potential to become a cornerstone of sustainable energy solutions.</p>","PeriodicalId":20401,"journal":{"name":"Preparative Biochemistry & Biotechnology","volume":" ","pages":"1-14"},"PeriodicalIF":2.0,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142829611","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":"Engineering <i>Escherichia coli</i> to metabolize sorbitol as the sole carbon source for synthesis of recombinant L-Asparaginase-II.","authors":"Dibya Ranjan Das, Shubhashree Mahalik","doi":"10.1080/10826068.2024.2440425","DOIUrl":"https://doi.org/10.1080/10826068.2024.2440425","url":null,"abstract":"<p><p>Sorbitol, known as D-Glucitol, is a hexose sugar alcohol that occurs naturally in various fruits, including berries, cherries, plums, pears, and apples. It is noteworthy that sorbitol can be metabolized by microbes, plants, and humans through distinct pathways. Nevertheless, in bacteria like <i>Escherichia coli</i> (<i>E. coli</i>), sorbitol is not the primary carbon source and its utilization is generally suppressed due to carbon catabolite repression. In this context, <i>Escherichia coli</i> has been engineered to enable the use of sorbitol as the sole carbon source for producing recombinant proteins. This modification involves a two-plasmid system where the sorbitol-6-phosphate dehydrogenase (<i>srlD</i>) gene is upregulated under an araBAD promoter, while the recombinant protein is expressed from a second plasmid under the tac promoter. The overexpression of <i>srlD</i> in the engineered <i>E. coli</i> strain enhances the utilization of sorbitol as the sole carbon source. When cultured in a medium supplemented solely with sorbitol, the engineered <i>E. coli</i> strain exhibits a 3.6 times higher specific growth rate and yields substantially higher concentration of recombinant protein compared to the wild-type strain. Additionally, the engineered strain demonstrates a higher Y<sub>P/X</sub> ratio than the wild-type strain.</p>","PeriodicalId":20401,"journal":{"name":"Preparative Biochemistry & Biotechnology","volume":" ","pages":"1-10"},"PeriodicalIF":2.0,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142822195","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}
Xiaolei Yang, Qi Li, Xiaoming Bai, Changning Li, Xuemei Li, Tuo Yao
{"title":"Optimal fermentation of <i>Pseudomonas synxantha</i> M1 and metabolomics analysis.","authors":"Xiaolei Yang, Qi Li, Xiaoming Bai, Changning Li, Xuemei Li, Tuo Yao","doi":"10.1080/10826068.2024.2428322","DOIUrl":"https://doi.org/10.1080/10826068.2024.2428322","url":null,"abstract":"<p><p>The microbial agents based on plant growth promoting rhizobacteria (PGPR) have become a hot topic in agricultural research, while the optimization of fermentation conditions for PGPR-based microbial agents still lack systematic research. The single-factor and orthogonal experiments were conducted to determine the optimal fermentation conditions of <i>Pseudomonas synxantha</i> M1. The results indicated that the glycerol and shaker speed was the most significant factors that influence the number of bacteria of <i>P. synxantha</i> M1 fermentation liquid. The viable bacteria count of microbial agent reached 7.1 × 10<sup>12</sup> cfu/mL at 36 h, which OD<sub>600</sub> value increased by 116.40% compared to before optimization, and promote the growth of highland barley. Significant differences of metabolites of fermentation liquid was observed in different fermentation times, including organic acids, lipids, and organoheterocyclic compounds using liquid chromatography tandem mass spectrometry (LC-MS/MS). In addition, the fermentation liquid was found to contain indoleacetic acid, glutathione and xanthine at the end of fermentation, which might contribute for the growth of plants as bioactive substances.</p>","PeriodicalId":20401,"journal":{"name":"Preparative Biochemistry & Biotechnology","volume":" ","pages":"1-11"},"PeriodicalIF":2.0,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142822218","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}
Jun Zhang, Ying Zhang, Wen Luo, Zhiyuan Wang, Pengmei Lv, Zhongming Wang
{"title":"A UHPLC-QE-MS-based metabolomics approach for the evaluation of fermented lipase by an engineered <i>Escherichia coli</i>.","authors":"Jun Zhang, Ying Zhang, Wen Luo, Zhiyuan Wang, Pengmei Lv, Zhongming Wang","doi":"10.1080/10826068.2024.2423665","DOIUrl":"https://doi.org/10.1080/10826068.2024.2423665","url":null,"abstract":"<p><p>Using an engineered <i>Escherichia coli</i> to produce lipase and can easily achieve high-level expression. The investigation of biochemical processes during lipase fermentation, approached from a metabolomics perspective, will yield novel insights into the efficient secretion of recombinant proteins. In this study, the lipase batch fermentation was carried out first with enzyme activity of 36.83 U/mg cells. Then, differential metabolites and metabolic pathways were identified using an untargeted metabolomics approach through comparative analysis of various fermentation periods. In total, 574 metabolites were identified: 545 were up-regulated and 29 were down-regulated, mainly in 153 organic acids and derivatives, 160 organoheterocyclic compounds, 64 lipids and lipid-like molecules, and 58 organic oxygen compounds. Through metabolic pathways and network analysis, it could be found that tryptophan metabolism was of great significance to lipase production, which could affect the secretion and synthesis of recombinant protein. In addition, the promotion effects of cell growth by varying concentrations of indole acetic acid serve to validate the results obtained from tryptophan metabolism. This study offers valuable insights into metabolic regulation of engineered <i>E. coli</i>, indicating that its fermentation bioprocess can be systematically designed according to metabolomics findings to enhance recombinant protein production.</p>","PeriodicalId":20401,"journal":{"name":"Preparative Biochemistry & Biotechnology","volume":" ","pages":"1-13"},"PeriodicalIF":2.0,"publicationDate":"2024-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142795003","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}
Jônatas de Carvalho-Silva, Ana Cláudia Vaz de Araújo, Pedro Miguel Ferreira-Santos, Attilio Converti, Tatiana Souza Porto
{"title":"Pectinase immobilized on magnetic nanoparticles coated with alginate for pectin hydrolysis in guava juice assisted by a stirred electromagnetic reactor.","authors":"Jônatas de Carvalho-Silva, Ana Cláudia Vaz de Araújo, Pedro Miguel Ferreira-Santos, Attilio Converti, Tatiana Souza Porto","doi":"10.1080/10826068.2024.2432389","DOIUrl":"https://doi.org/10.1080/10826068.2024.2432389","url":null,"abstract":"<p><p><i>Aspergillus aculeatus</i> pectinase was immobilized on magnetic nanoparticles coated with calcium alginate for pectin hydrolysis in guava juice by a stirred electromagnetic reactor (SER). The average crystallite size estimated by the Scherrer formula was 33.7 nm. The reaction rate in SER (701.7 U/mL) was almost twice that of the static process (362.5 U/mL). Both processes displayed a sigmoidal trend with positive cooperativity (<i>n</i>) of 5 and 4, respectively. Both free and immobilized pectinase showed great performance in the pH range of 4.0-7.0. After immobilization, pectinase acted optimally at 50 °C. Pectin hydrolysis was performed for over 10 successive cycles in SER losing only 30% of its initial activity. Thermodynamic activation parameters of the reaction revealed higher spontaneity and efficiency when hydrolysis was performed in SER. Pectin hydrolysis in guava juice displayed 41% turbidity and 85.5% viscosity reduction. The electromagnetic reactor displayed great potential for performing hydrolysis of pectin in guava juice. The biocatalyst showed good features for further applications in food industries.</p>","PeriodicalId":20401,"journal":{"name":"Preparative Biochemistry & Biotechnology","volume":" ","pages":"1-14"},"PeriodicalIF":2.0,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142710791","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}
Hui-Seon Yun, Eun-Jung Kim, Byung-Gee Kim, Hee-Jin Jeong
{"title":"Convenient production of a novel recombinant antibody against periodontitis biomarker S100A8.","authors":"Hui-Seon Yun, Eun-Jung Kim, Byung-Gee Kim, Hee-Jin Jeong","doi":"10.1080/10826068.2024.2430615","DOIUrl":"https://doi.org/10.1080/10826068.2024.2430615","url":null,"abstract":"<p><p>S100A8 serves as a biomarker for periodontitis and is involved in inflammatory processes, making its detection highly important. In this study, we produced recombinant 5A11 (r5A11) through mammalian cell culture. By employing a three-step process of transfection, suspension cell culture, and purification, we conveniently produced r5A11 with high yield and purity. The limit of detection for the r5A11-based immunoassay was 1.7 ± 0.2 × 10<sup>-1 </sup>ng/mL, which was higher than that of the commercially available anti-S100A8 antibody. These findings suggest the potential use of this novel antibody in various research applications and practical approaches for simple and sensitive S100A8 detection.</p>","PeriodicalId":20401,"journal":{"name":"Preparative Biochemistry & Biotechnology","volume":" ","pages":"1-6"},"PeriodicalIF":2.0,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142676639","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}
Anubhuti Kawatra, Bharti Datten, Rupesh Hans, Pooja Gulati
{"title":"Hybrid magnetic nanocomposites of arginine deiminase with improved stability and recyclability for biomedical applications.","authors":"Anubhuti Kawatra, Bharti Datten, Rupesh Hans, Pooja Gulati","doi":"10.1080/10826068.2024.2430626","DOIUrl":"10.1080/10826068.2024.2430626","url":null,"abstract":"<p><p>Nanocarrier-based immobilization has created new avenues for enhancing the biophysical properties of enzymes. Nanomatrices such as magnetite nanoparticles (MNPs), chitin, and chitosan with large surface areas and tunable morphology have been developed to circumvent the bottlenecks of free enzymes. The present study used MNPs to immobilize the enzyme arginine deiminase (ADI) for improved morphological control, recovery, operational stability, and easy recyclability. Hybrid magnetic arginine deiminase cross-linked enzyme aggregate (mADI-CLEA) was developed for the first time by co-aggregating ADI with magnetite nanocomposites, followed by its cross-linkage with glutaraldehyde. Structural analysis by DLS/ZETA, SEM, and FT-IR revealed their highly stable and robust nature. The resulting mADI-CLEA exhibited higher pH resistivity and thermostability than ADI-CLEA. Reusability and storage stability assay indicated that mADI-CLEA maintained more than 60% residual activity even after seven batch cycles and was stable for more than 70 days. These hybrid magnetic aggregates of ADI offer an economical and stable alternative for biomedical applications of ADI.</p>","PeriodicalId":20401,"journal":{"name":"Preparative Biochemistry & Biotechnology","volume":" ","pages":"1-8"},"PeriodicalIF":2.0,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668228","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":"Cellulase immobilization on nano-chitosan/chromium metal-organic framework hybrid matrix for efficient conversion of lignocellulosic biomass to glucose.","authors":"Shashi Suhag, Utkarsh Jain, Nidhi Chauhan, Vinita Hooda","doi":"10.1080/10826068.2024.2425970","DOIUrl":"https://doi.org/10.1080/10826068.2024.2425970","url":null,"abstract":"<p><p>In the current work, cellulase from <i>Aspergillus niger</i> was successfully immobilized on a novel epoxy-affixed chromium metal-organic framework/chitosan (Cr@-MIL-101/CS) support via covalent method using glutaraldehyde as a crosslinker. The bare and cellulase-bound support was characterized by using various microscopic and spectroscopic techniques. Immobilized cellulase exhibited a high immobilization yield of 0.7 ± 0.01 mg/cm<sup>2</sup>, retaining 87.5 ± 0.04% of its specific activity and displaying enhanced catalytic performance. The immobilized enzyme was maximally active at pH 5.0, temperature 65 °C and 0.9 × 10-2 mg/ml saturating substrate concentration and the half-lives of free and immobilized cellulases were approximately 9 and 19 days, respectively. The decrease in activation energy, enthalpy change, and Gibbs free energy change, coupled with an increase in entropy change upon immobilization, indicated that the enzyme's efficiency, stability, and spontaneity in catalyzing the reaction were enhanced by immobilization. Additionally, the immobilized cellulase efficiently converted rice husk cellulose to glucose, with a quantification limit of 0.05%, linear measurement ranging from 0.1 to 0.9%, and 8.5% conversion efficiency. The present method exhibited a strong correlation (R<sup>2</sup> = 0.998) with the DNS method, validating its reliability. Notably, the epoxy/Cr@-MIL-101/CS-bound cellulase demonstrated impressive thermal and pH stabilities, retaining 50% of its activity at 75 °C and over 96% at pH levels of 4.5 and 5.0 after 12 h. Furthermore, it showed excellent reusability, preserving 80% of its activity after 15 cycles and maintaining 50% of its activity even after 20 days of storage. These results suggest that epoxy/Cr@-MIL-101/CS/cellulase composites could be very effective for large-scale cellulose hydrolysis applications.</p>","PeriodicalId":20401,"journal":{"name":"Preparative Biochemistry & Biotechnology","volume":" ","pages":"1-21"},"PeriodicalIF":2.0,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142626492","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}
Yeganeh Shirazi, Salar Helchi, Mir Mehrshad Emamshoushtari, Sina Niakan, Elnaz Sohani, Farshid Pajoum Shariati
{"title":"The effect of different light spectra on selenium bioaccumulation by <i>Spirulina platensis</i> cyanobacteria in flat plate photobioreactors.","authors":"Yeganeh Shirazi, Salar Helchi, Mir Mehrshad Emamshoushtari, Sina Niakan, Elnaz Sohani, Farshid Pajoum Shariati","doi":"10.1080/10826068.2024.2426744","DOIUrl":"https://doi.org/10.1080/10826068.2024.2426744","url":null,"abstract":"<p><p>Selenium (Se) plays a crucial role in human health, influencing conditions such as cancer, diabetes, and neurological disorders. With global population growth and unequal nutrient distribution threatening food security, new approaches are needed to meet the nutritional needs of the world. Se is essential for immune function, metabolism, and antioxidant defense, and in regions suffering from food insecurity and malnutrition, selenium-enriched food could offer an affordable solution. <i>Spirulina platensis</i>, microalgae, can bioaccumulate Se from its environment, enhancing its nutritional value. This study explores how different light spectra (red, white, yellow, and blue LEDs) affect Se bioaccumulation in <i>Spirulina</i> when Na<sub>2</sub>SeO<sub>3</sub> is added to the culture medium in photobioreactors. The results show that red light made the highest Se bioaccumulation (0.118 mg.L<sup>-1</sup>), followed by white, yellow, and blue light. Se addition also increased cell dry weight by 46%, 33%, 22%, and 60%, respectively, compared to photobioreactors without Se, with biomass productivity highest under red light. Furthermore, Se boosted maximum Chl α concentration, improving photosynthetic efficiency. These findings suggest that optimizing light conditions can significantly enhance the nutritional value of <i>Spirulina</i>, offering a potential solution to global hunger by providing a sustainable, selenium-enriched food source.</p>","PeriodicalId":20401,"journal":{"name":"Preparative Biochemistry & Biotechnology","volume":" ","pages":"1-11"},"PeriodicalIF":2.0,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142626496","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}