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BioTech, Volume 13, Issue 1 (March 2024) – 7 articles

Cover Story (view full-size image): Gene therapy holds promise as a life-changing option for individuals with genetic variants. FDA-approved gene therapies have generated buzz around the ability to change the course of genetic syndromes. However, this excitement risks over-expansion into areas of genetic disease that may not fit the current state of gene therapy. It is critical to evaluate the field of genetic diseases relative to the continued risks of delivery systems and foreign RNA, performing cost–benefit analyses for each gene therapy use. Within the work by Henderson et al., they present the current state while setting forth tools and resources to guide informed directions to avoid foreseeable issues in gene therapy that could prevent continued success in the field. View this paper
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14 pages, 7442 KiB  
Article
Optimization of Aqueous Extraction of Polyphenols from Cuminum cyminum Seeds Using Response Surface Methodology and Assessment of Biological Activity
by Hana El Tannir, Diana Houhou, Espérance Debs, Mohamed Koubaa, Adla Jammoul, Bilal Azakir, Mahmoud I. Khalil, Nada El Darra and Nicolas Louka
BioTech 2024, 13(1), 7; https://doi.org/10.3390/biotech13010007 - 21 Mar 2024
Viewed by 660
Abstract
(1) Background: Cumin seeds, extracted from the plant Cuminum cyminum, are abundant in phenolic compounds and have been extensively researched for their chemical makeup and biological effects. The objective of this research is to enhance the water extraction of polyphenols through the [...] Read more.
(1) Background: Cumin seeds, extracted from the plant Cuminum cyminum, are abundant in phenolic compounds and have been extensively researched for their chemical makeup and biological effects. The objective of this research is to enhance the water extraction of polyphenols through the water bath (WB) technique and to evaluate the antiradical, antibacterial, and anticancer effects of the extract. (2) Methods: Response Surface Methodology was used to find the best parameters to extract polyphenols. Three experimental parameters, time, temperature, and solid-liquid ratio, were tested. The disc diffusion method has been used to determine the antimicrobial activities against Salmonella Typhimurium, Pseudomonas aeruginosa, Escherichia coli, Staphylococcus aureus, and Candida albicans. The antiradical activity was performed using the DPPH method, while total phenolic content was performed using Folin–Ciocalteu. High-Performance Liquid Chromatography (HPLC) was conducted to analyze the phytochemical profile of WB extracts. The anticancer activity of the lyophilized extract was assessed against three cancer cell lines (colon (HT29), lung (A549), and breast (MCF7) cancer cell lines).; (3) Results: The optimal conditions for water extraction were 130 min at 72 °C. The total phenolic compounds yield (14.7 mg GAE/g DM) and antioxidant activity (0.52 mg trolox eq./mL) were obtained using a 1:40 solid–liquid ratio. The primary polyphenols identified were the flavonoids rutin (0.1 ppm) and ellagic acid (3.78 ppm). The extract had no antibacterial or antifungal activities against the microorganisms tested. The extract showed anticancer activity of about 98% against MCF7 (breast cancer cell line), about 81% against HT29 (colon cancer cell line), and 85% against A549 (lung cancer cell line) at high doses. (4) Conclusions: Extraction time and a high solid–liquid ratio had a positive impact on polyphenol recovery and in maintaining their quantity and quality. Furthermore, the optimal aqueous extract exhibited strong antiradical activity reflected by the inhibition of free radicals in addition to a significant specificity against the tested cancer cell lines. Full article
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11 pages, 1824 KiB  
Article
Effect of Chitosan Degradation Products, Glucosamine and Chitosan Oligosaccharide, on Osteoclastic Differentiation
by Tomoharu Takeuchi, Midori Oyama and Tomomi Hatanaka
BioTech 2024, 13(1), 6; https://doi.org/10.3390/biotech13010006 - 06 Mar 2024
Viewed by 512
Abstract
Chitosan, a natural cationic polysaccharide derived from crustaceans and shellfish shells, is known for its advantageous biological properties, including biodegradability, biocompatibility, and antibacterial activity. Chitosan and its composite materials are studied for their potential for bone tissue repair. However, the effects of chitosan [...] Read more.
Chitosan, a natural cationic polysaccharide derived from crustaceans and shellfish shells, is known for its advantageous biological properties, including biodegradability, biocompatibility, and antibacterial activity. Chitosan and its composite materials are studied for their potential for bone tissue repair. However, the effects of chitosan degradation products, glucosamine (GlcN) and chitosan oligosaccharide (COS), on osteoclasts remain unclear. If these chitosan degradation products promote osteoclastic differentiation, careful consideration is required for the use of chitosan and related materials in bone repair applications. Here, we assessed the effects of high (500 μg/mL) and low (0.5 μg/mL) concentrations of GlcN and COS on osteoclastic differentiation in human peripheral blood mononuclear cells (PBMCs) and murine macrophage-like RAW264 cells. A tartrate-resistant acid phosphatase (TRAP) enzyme activity assay, TRAP staining, and actin staining were used to assess osteoclastic differentiation. High concentrations of GlcN and COS, but not low concentrations, suppressed macrophage colony-stimulating factor (M-CSF)- and RANKL-dependent increases in TRAP enzyme activity, TRAP-positive multinuclear osteoclast formation, and actin ring formation in PBMCs without cytotoxicity. Similar effects were observed in the RANKL-dependent osteoclastic differentiation of RAW264 cells. In conclusion, chitosan degradation products do not possess osteoclast-inducing properties, suggesting that chitosan and its composite materials can be safely used for bone tissue repair. Full article
(This article belongs to the Section Medical Biotechnology)
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22 pages, 6055 KiB  
Article
Susceptibility of Tetranychus urticae to the Alkaloidal Extract of Zanthoxylum schreberi Bark: Phenotypic and Biochemical Insights for Biotechnological Exploitation
by Ricardo A. Rincón, Daniel Rodríguez and Ericsson Coy-Barrera
BioTech 2024, 13(1), 5; https://doi.org/10.3390/biotech13010005 - 20 Feb 2024
Viewed by 696
Abstract
Tetranychus urticae Koch, a phytophagous mite, is one of the most significant crop pests globally. The primary method employed for controlling T. urticae involves chemical means, utilizing synthesized products, posing the risk of developing resistance. The urgency for novel strategies integrated into pest [...] Read more.
Tetranychus urticae Koch, a phytophagous mite, is one of the most significant crop pests globally. The primary method employed for controlling T. urticae involves chemical means, utilizing synthesized products, posing the risk of developing resistance. The urgency for novel strategies integrated into pest management programs to combat this mite is becoming increasingly imperative. Botanical pesticides emerge as a promising tool to forestall arthropod resistance. Among these, extracts from Rutaceae plants, abundant in bioactive specialized metabolites, have demonstrated potential as insecticides and miticides. In this study, various concentrations of alkaloidal extracts sourced from the bark of Zanthoxylum schreberi J.F.Gmel. (Rutaceae) were evaluated against T. urticae adult females. Furthermore, the extract’s combination with three distinct commercial acaricides (i.e., chlorfenapyr, cyflumetofen, and abamectin) was also assessed for this mite. Chemical characterization of the extract via LC-MS allowed for the annotation of various compounds related to ten benzylisoquinoline-derived alkaloids. The extract, both alone and in combination with commercial insecticides, yielded varying responses, inducing over 40% mortality at 2% w/w, demonstrating a 90% repellency rate at the same concentration, and exerting a moderate impact on fecundity. These treatments extended beyond phenotypic responses, delving into the biochemical effects on treated T. urticae females through an exploration of the impact on four enzymes, i.e., acetylcholinesterase (AChE), glutathione S-transferase (GST), esterases (GE), and P450-like monooxygenases (PMO). Employing consensus docking studies and in vitro enzymatic evaluations, it was discovered that the Z. schreberi-derived extract and its constituents significantly affected two key enzymes, AChE and GST (IC50 < 6 µM), which were associated with the phenotypic observations of T. urticae females. The evaluation of alkaloid-rich botanicals showcases promising potential as a relevant biotechnological strategy in addressing mite-related concerns, offering a pathway toward innovative and sustainable pest management solutions. Full article
(This article belongs to the Section Agricultural and Food Biotechnology)
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31 pages, 9703 KiB  
Article
Expression and Purification of Cp3GT: Structural Analysis and Modeling of a Key Plant Flavonol-3-O Glucosyltransferase from Citrus paradisi
by Aaron S. Birchfield and Cecilia A. McIntosh
BioTech 2024, 13(1), 4; https://doi.org/10.3390/biotech13010004 - 07 Feb 2024
Viewed by 697
Abstract
Glycosyltransferases (GTs) are pivotal enzymes in the biosynthesis of various biological molecules. This study focuses on the scale-up, expression, and purification of a plant flavonol-specific 3-O glucosyltransferase (Cp3GT), a key enzyme from Citrus paradisi, for structural analysis and modeling. The challenges associated [...] Read more.
Glycosyltransferases (GTs) are pivotal enzymes in the biosynthesis of various biological molecules. This study focuses on the scale-up, expression, and purification of a plant flavonol-specific 3-O glucosyltransferase (Cp3GT), a key enzyme from Citrus paradisi, for structural analysis and modeling. The challenges associated with recombinant protein production in Pichia pastoris, such as proteolytic degradation, were addressed through the optimization of culture conditions and purification processes. The purification strategy employed affinity, anion exchange, and size exclusion chromatography, leading to greater than 95% homogeneity for Cp3GT. In silico modeling, using D-I-TASSER and COFACTOR integrated with the AlphaFold2 pipeline, provided insights into the structural dynamics of Cp3GT and its ligand binding sites, offering predictions for enzyme–substrate interactions. These models were compared to experimentally derived structures, enhancing understanding of the enzyme’s functional mechanisms. The findings present a comprehensive approach to produce a highly purified Cp3GT which is suitable for crystallographic studies and to shed light on the structural basis of flavonol specificity in plant GTs. The significant implications of these results for synthetic biology and enzyme engineering in pharmaceutical applications are also considered. Full article
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12 pages, 932 KiB  
Review
Exploring DNA Damage and Repair Mechanisms: A Review with Computational Insights
by Jiawei Chen, Ravi Potlapalli, Heng Quan, Lingtao Chen, Ying Xie, Seyedamin Pouriyeh, Nazmus Sakib, Lichao Liu and Yixin Xie
BioTech 2024, 13(1), 3; https://doi.org/10.3390/biotech13010003 - 16 Jan 2024
Viewed by 1538
Abstract
DNA damage is a critical factor contributing to genetic alterations, directly affecting human health, including developing diseases such as cancer and age-related disorders. DNA repair mechanisms play a pivotal role in safeguarding genetic integrity and preventing the onset of these ailments. Over the [...] Read more.
DNA damage is a critical factor contributing to genetic alterations, directly affecting human health, including developing diseases such as cancer and age-related disorders. DNA repair mechanisms play a pivotal role in safeguarding genetic integrity and preventing the onset of these ailments. Over the past decade, substantial progress and pivotal discoveries have been achieved in DNA damage and repair. This comprehensive review paper consolidates research efforts, focusing on DNA repair mechanisms, computational research methods, and associated databases. Our work is a valuable resource for scientists and researchers engaged in computational DNA research, offering the latest insights into DNA-related proteins, diseases, and cutting-edge methodologies. The review addresses key questions, including the major types of DNA damage, common DNA repair mechanisms, the availability of reliable databases for DNA damage and associated diseases, and the predominant computational research methods for enzymes involved in DNA damage and repair. Full article
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12 pages, 2031 KiB  
Article
Styrene Production in Genetically Engineered Escherichia coli in a Two-Phase Culture
by Shuhei Noda, Ryosuke Fujiwara, Yutaro Mori, Mayumi Dainin, Tomokazu Shirai and Akihiko Kondo
BioTech 2024, 13(1), 2; https://doi.org/10.3390/biotech13010002 - 14 Jan 2024
Viewed by 1020
Abstract
Styrene is an important industrial chemical. Although several studies have reported microbial styrene production, the amount of styrene produced in batch cultures can be increased. In this study, styrene was produced using genetically engineered Escherichia coli. First, we evaluated five types of [...] Read more.
Styrene is an important industrial chemical. Although several studies have reported microbial styrene production, the amount of styrene produced in batch cultures can be increased. In this study, styrene was produced using genetically engineered Escherichia coli. First, we evaluated five types of phenylalanine ammonia lyases (PALs) from Arabidopsis thaliana (AtPAL) and Brachypodium distachyon (BdPAL) for their ability to produce trans-cinnamic acid (Cin), a styrene precursor. AtPAL2-expressing E. coli produced approximately 700 mg/L of Cin and we found that BdPALs could convert Cin into styrene. To assess styrene production, we constructed an E. coli strain that co-expressed AtPAL2 and ferulic acid decarboxylase from Saccharomyces cerevisiae. After a biphasic culture with oleyl alcohol, styrene production and yield from glucose were 3.1 g/L and 26.7% (mol/mol), respectively, which, to the best of our knowledge, are the highest values obtained in batch cultivation. Thus, this strain can be applied to the large–scale industrial production of styrene. Full article
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31 pages, 4942 KiB  
Review
Gene Therapy for Genetic Syndromes: Understanding the Current State to Guide Future Care
by Marian L. Henderson, Jacob K. Zieba, Xiaopeng Li, Daniel B. Campbell, Michael R. Williams, Daniel L. Vogt, Caleb P. Bupp, Yvonne M. Edgerly, Surender Rajasekaran, Nicholas L. Hartog, Jeremy W. Prokop and Jena M. Krueger
BioTech 2024, 13(1), 1; https://doi.org/10.3390/biotech13010001 - 03 Jan 2024
Cited by 2 | Viewed by 3142
Abstract
Gene therapy holds promise as a life-changing option for individuals with genetic variants that give rise to disease. FDA-approved gene therapies for Spinal Muscular Atrophy (SMA), cerebral adrenoleukodystrophy, β-Thalassemia, hemophilia A/B, retinal dystrophy, and Duchenne Muscular Dystrophy have generated buzz around the ability [...] Read more.
Gene therapy holds promise as a life-changing option for individuals with genetic variants that give rise to disease. FDA-approved gene therapies for Spinal Muscular Atrophy (SMA), cerebral adrenoleukodystrophy, β-Thalassemia, hemophilia A/B, retinal dystrophy, and Duchenne Muscular Dystrophy have generated buzz around the ability to change the course of genetic syndromes. However, this excitement risks over-expansion into areas of genetic disease that may not fit the current state of gene therapy. While in situ (targeted to an area) and ex vivo (removal of cells, delivery, and administration of cells) approaches show promise, they have a limited target ability. Broader in vivo gene therapy trials have shown various continued challenges, including immune response, use of immune suppressants correlating to secondary infections, unknown outcomes of overexpression, and challenges in driving tissue-specific corrections. Viral delivery systems can be associated with adverse outcomes such as hepatotoxicity and lethality if uncontrolled. In some cases, these risks are far outweighed by the potentially lethal syndromes for which these systems are being developed. Therefore, it is critical to evaluate the field of genetic diseases to perform cost–benefit analyses for gene therapy. In this work, we present the current state while setting forth tools and resources to guide informed directions to avoid foreseeable issues in gene therapy that could prevent the field from continued success. Full article
(This article belongs to the Special Issue Biotechnology and Bioethics)
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