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BioTech, Volume 12, Issue 3 (September 2023) – 11 articles

Cover Story (view full-size image): The hallmark of targeted cancer cell death suggests a therapeutic advantage to targeted protein degradation strategies; the fewer surviving cancer cells there are, the fewer mutants there will be that are resistant to chemotherapy. View this paper
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11 pages, 1850 KiB  
Article
Shikonin and Juglone Inhibit Mycobacterium tuberculosis Low-Molecular-Weight Protein Tyrosine Phosphatase a (Mt-PTPa)
by Abdulhakeem O. Sulyman, Jessie Fulcher, Samuel Crossley, Amos A. Fatokun and Femi J. Olorunniji
BioTech 2023, 12(3), 59; https://doi.org/10.3390/biotech12030059 - 20 Sep 2023
Cited by 1 | Viewed by 1421
Abstract
Low-molecular-weight protein tyrosine phosphatases (LMW-PTPs) are involved in promoting the intracellular survival of Mycobacterium tuberculosis (Mtb), the causative organism of tuberculosis. These PTPs directly alter host signalling pathways to evade the hostile environment of macrophages and avoid host clearance. Among these, protein tyrosine [...] Read more.
Low-molecular-weight protein tyrosine phosphatases (LMW-PTPs) are involved in promoting the intracellular survival of Mycobacterium tuberculosis (Mtb), the causative organism of tuberculosis. These PTPs directly alter host signalling pathways to evade the hostile environment of macrophages and avoid host clearance. Among these, protein tyrosine phosphatase A (Mt-PTPa) is implicated in phagosome acidification failure, thereby inhibiting phagosome maturation to promote Mycobacterium tuberculosis (Mtb) survival. In this study, we explored Mt-PTPa as a potential drug target for treating Mtb. We started by screening a library of 502 pure natural compounds against the activities of Mt-PTPa in vitro, with a threshold of 50% inhibition of activity via a <500 µM concentration of the candidate drugs. The initial screen identified epigallocatechin, myricetin, rosmarinic acid, and shikonin as hits. Among these, the naphthoquinone, shikonin (5, 8-dihydroxy-2-[(1R)-1-hydroxy-4-methyl-3-pentenyl]-1,4-naphthoquinone), showed the strongest inhibition (IC50 33 µM). Further tests showed that juglone (5-hydroxy-1,4-naphthalenedione), another naphthoquinone, displayed similar potent inhibition of Mt-PTPa to shikonin. Kinetic analysis of the inhibition patterns suggests a non-competitive inhibition mechanism for both compounds, with inhibitor constants (Ki) of 8.5 µM and 12.5 µM for shikonin and juglone, respectively. Our findings are consistent with earlier studies suggesting that Mt-PTPa is susceptible to specific allosteric modulation via a non-competitive or mixed inhibition mechanism. Full article
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11 pages, 1436 KiB  
Article
Assessing Curcumin Uptake and Clearance and Their Influence on Superoxide Dismutase Activity in Drosophila melanogaster
by Tammy R. Hoffman, Sarah A. Emsley, Jenna C. Douglas, Kaela R. Reed, Abigail R. Esquivel, Marc J. Koyack, Brie E. Paddock and Patrick Videau
BioTech 2023, 12(3), 58; https://doi.org/10.3390/biotech12030058 - 08 Sep 2023
Viewed by 1151
Abstract
While normal levels of reactive oxygen and nitrogen species (RONS) are required for proper organismal function, increased levels result in oxidative stress. Oxidative stress may be managed via the scavenging activities of antioxidants (e.g., curcumin) and the action of enzymes, including superoxide dismutase [...] Read more.
While normal levels of reactive oxygen and nitrogen species (RONS) are required for proper organismal function, increased levels result in oxidative stress. Oxidative stress may be managed via the scavenging activities of antioxidants (e.g., curcumin) and the action of enzymes, including superoxide dismutase (SOD). In this work, the uptake and clearance of dietary curcuminoids (consisting of curcumin, demethoxycurcumin, and bisdemethoxycurcumin) was assessed in Drosophila melanogaster larvae following chronic or acute exposure. High levels of curcuminoid uptake and loss were observed within a few hours and leveled off within eight hours post treatment onset. The addition or removal of curcuminoids from media resulted in corresponding changes in SOD activity, and the involvement of each of the three SOD genes was assessed for their contribution to total SOD activity. Taken together, these data provide insight into the uptake and clearance dynamics of curcuminoids and indicate that, while SOD activity generally increases following curcuminoid treatment, the individual SOD genes appear to contribute differently to this response. Full article
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23 pages, 3365 KiB  
Review
Targeted Strategies for Degradation of Key Transmembrane Proteins in Cancer
by Vehary Sakanyan, Nina Iradyan and Rodolphe Alves de Sousa
BioTech 2023, 12(3), 57; https://doi.org/10.3390/biotech12030057 - 06 Sep 2023
Viewed by 2514
Abstract
Targeted protein degradation is an attractive technology for cancer treatment due to its ability to overcome the unpredictability of the small molecule inhibitors that cause resistance mutations. In recent years, various targeted protein degradation strategies have been developed based on the ubiquitin–proteasome system [...] Read more.
Targeted protein degradation is an attractive technology for cancer treatment due to its ability to overcome the unpredictability of the small molecule inhibitors that cause resistance mutations. In recent years, various targeted protein degradation strategies have been developed based on the ubiquitin–proteasome system in the cytoplasm or the autophagy–lysosomal system during endocytosis. In this review, we describe and compare technologies for the targeted inhibition and targeted degradation of the epidermal growth factor receptor (EGFR), one of the major proteins responsible for the onset and progression of many types of cancer. In addition, we develop an alternative strategy, called alloAUTO, based on the binding of new heterocyclic compounds to an allosteric site located in close proximity to the EGFR catalytic site. These compounds cause the targeted degradation of the transmembrane receptor, simultaneously activating both systems of protein degradation in cells. Damage to the EGFR signaling pathways promotes the inactivation of Bim sensor protein phosphorylation, which leads to the disintegration of the cytoskeleton, followed by the detachment of cancer cells from the extracellular matrix, and, ultimately, to cancer cell death. This hallmark of targeted cancer cell death suggests an advantage over other targeted protein degradation strategies, namely, the fewer cancer cells that survive mean fewer chemotherapy-resistant mutants appear. Full article
(This article belongs to the Special Issue Feature Papers in Medical Biotechnology)
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18 pages, 1283 KiB  
Review
Benchmarking RNA Editing Detection Tools
by David Rodríguez Morales, Sarah Rennie and Shizuka Uchida
BioTech 2023, 12(3), 56; https://doi.org/10.3390/biotech12030056 - 26 Aug 2023
Viewed by 2462
Abstract
RNA, like DNA and proteins, can undergo modifications. To date, over 170 RNA modifications have been identified, leading to the emergence of a new research area known as epitranscriptomics. RNA editing is the most frequent RNA modification in mammalian transcriptomes, and two types [...] Read more.
RNA, like DNA and proteins, can undergo modifications. To date, over 170 RNA modifications have been identified, leading to the emergence of a new research area known as epitranscriptomics. RNA editing is the most frequent RNA modification in mammalian transcriptomes, and two types have been identified: (1) the most frequent, adenosine to inosine (A-to-I); and (2) the less frequent, cysteine to uracil (C-to-U) RNA editing. Unlike other epitranscriptomic marks, RNA editing can be readily detected from RNA sequencing (RNA-seq) data without any chemical conversions of RNA before sequencing library preparation. Furthermore, analyzing RNA editing patterns from transcriptomic data provides an additional layer of information about the epitranscriptome. As the significance of epitranscriptomics, particularly RNA editing, gains recognition in various fields of biology and medicine, there is a growing interest in detecting RNA editing sites (RES) by analyzing RNA-seq data. To cope with this increased interest, several bioinformatic tools are available. However, each tool has its advantages and disadvantages, which makes the choice of the most appropriate tool for bench scientists and clinicians difficult. Here, we have benchmarked bioinformatic tools to detect RES from RNA-seq data. We provide a comprehensive view of each tool and its performance using previously published RNA-seq data to suggest recommendations on the most appropriate for utilization in future studies. Full article
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14 pages, 10310 KiB  
Article
Chitosan Sponges for Efficient Accumulation and Controlled Release of C-Phycocyanin
by Yana E. Sergeeva, Anastasia A. Zakharevich, Daniil V. Sukhinov, Alexandra I. Koshkalda, Mariya V. Kryukova, Sergey N. Malakhov, Christina G. Antipova, Olga I. Klein, Pavel M. Gotovtsev and Timofei E. Grigoriev
BioTech 2023, 12(3), 55; https://doi.org/10.3390/biotech12030055 - 17 Aug 2023
Cited by 2 | Viewed by 1758
Abstract
The paper proposed a new porous material for wound healing based on chitosan and C-phycocyanin (C-PC). In this work, C-PC was extracted from the cyanobacteria Arthrospira platensis biomass and purified through ammonium sulfate precipitation. The obtained C-PC with a purity index (PI) of [...] Read more.
The paper proposed a new porous material for wound healing based on chitosan and C-phycocyanin (C-PC). In this work, C-PC was extracted from the cyanobacteria Arthrospira platensis biomass and purified through ammonium sulfate precipitation. The obtained C-PC with a purity index (PI) of 3.36 ± 0.24 was loaded into a chitosan sponge from aqueous solutions of various concentrations (250, 500, and 1000 mg/L). According to the FTIR study, chitosan did not form new bonds with C-PC, but acted as a carrier. The encapsulation efficiency value exceeded 90%, and the maximum loading capacity was 172.67 ± 0.47 mg/g. The release of C-PC from the polymer matrix into the saline medium was estimated, and it was found 50% of C-PC was released in the first hour and the maximum concentration was reached in 5–7 h after the sponge immersion. The PI of the released C-PC was 3.79 and 4.43 depending on the concentration of the initial solution. Full article
(This article belongs to the Section Medical Biotechnology)
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14 pages, 1419 KiB  
Article
Characterization of Enzyme-Linked Immunosorbent Assay (ELISA) for Quantification of Antibodies against Salmonella Typhimurium and Salmonella Enteritidis O-Antigens in Human Sera
by Maria Grazia Aruta, Elisa Lari, Daniele De Simone, Bianca Semplici, Claudia Semplici, Helen Dale, Esmelda Chirwa, Innocent Kadwala, Maurice Mbewe, Happy Banda, Miren Iturriza-Gomara, Melita Gordon, Tonney Nyirenda, Pietro Piu, Mariagrazia Pizza, Francesco Berlanda Scorza, Silvia Grappi, Rocío Canals, Omar Rossi and on behalf of the Vacc-iNTS Consortium Collaborators
BioTech 2023, 12(3), 54; https://doi.org/10.3390/biotech12030054 - 11 Aug 2023
Viewed by 2332
Abstract
Nontyphoidal Salmonella (NTS) is a leading cause of morbidity and mortality caused by enteric pathogens worldwide in both children and adults, and vaccines are not yet available. The measurement of antigen-specific antibodies in the sera of vaccinated or convalescent individuals is crucial to [...] Read more.
Nontyphoidal Salmonella (NTS) is a leading cause of morbidity and mortality caused by enteric pathogens worldwide in both children and adults, and vaccines are not yet available. The measurement of antigen-specific antibodies in the sera of vaccinated or convalescent individuals is crucial to understand the incidence of disease and the immunogenicity of vaccine candidates. A solid and standardized assay used to determine the level of specific anti-antigens IgG is therefore of paramount importance. In this work, we presented the characterization of a customized enzyme-linked immunosorbent assay (ELISA) with continuous readouts and a standardized definition of EU/mL. We assessed various performance parameters: standard curve accuracy, dilutional linearity, intermediate precision, specificity, limits of blanks, and quantification. The simplicity of the assay, its high sensitivity and specificity coupled with its low cost and the use of basic consumables and instruments without the need of high automation makes it suitable for transfer and application to different laboratories, including resource-limiting settings where the disease is endemic. This ELISA is, therefore, fit for purpose to be used for quantification of antibodies against Salmonella Typhimurium and Salmonella Enteritidis O-antigens in human samples, both for vaccine clinical trials and large sero-epidemiological studies. Full article
(This article belongs to the Section Medical Biotechnology)
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20 pages, 1607 KiB  
Article
Growth Efficiency of Chlorella sorokiniana in Synthetic Media and Unsterilized Domestic Wastewater
by Svetlana S. Bulynina, Elvira E. Ziganshina and Ayrat M. Ziganshin
BioTech 2023, 12(3), 53; https://doi.org/10.3390/biotech12030053 - 03 Aug 2023
Cited by 4 | Viewed by 2473
Abstract
Incorporating a variety of microalgae into wastewater treatment is considered an economically viable and environmentally sound strategy. The present work assessed the growth characteristics of Chlorella sorokiniana during cultivation in balanced synthetic media and domestic wastewater. Increasing the NH4+–N concentration [...] Read more.
Incorporating a variety of microalgae into wastewater treatment is considered an economically viable and environmentally sound strategy. The present work assessed the growth characteristics of Chlorella sorokiniana during cultivation in balanced synthetic media and domestic wastewater. Increasing the NH4+–N concentration to 360 mg L−1 and adding extra PO43−–P and SO42−–S (up to 80 and 36 mg L−1, respectively) contributed to an increase in the total biomass levels (5.7–5.9 g L−1) during the cultivation of C. sorokiniana in synthetic media. Under these conditions, the maximum concentrations of chlorophylls and carotenoids were 180 ± 7.5 and 26 ± 1.4 mg L−1, respectively. Furthermore, when studying three types of domestic wastewaters, it was noted that only one wastewater contributed to the productive growth of C. sorokiniana, but all wastewaters stimulated an increased accumulation of protein. Finally, the alga, when growing in optimal unsterilized wastewater, showed a maximum specific growth rate of 0.73 day−1, a biomass productivity of 0.21 g L−1 day−1, and 100% NH4+–N removal. These results demonstrate that the tested alga actively adapts to changes in the composition of the growth medium and accumulates high levels of protein in systems with poor-quality water. Full article
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12 pages, 396 KiB  
Article
Categorical Data Analysis for High-Dimensional Sparse Gene Expression Data
by Niloufar Dousti Mousavi, Hani Aldirawi and Jie Yang
BioTech 2023, 12(3), 52; https://doi.org/10.3390/biotech12030052 - 27 Jul 2023
Cited by 1 | Viewed by 1568
Abstract
Categorical data analysis becomes challenging when high-dimensional sparse covariates are involved, which is often the case for omics data. We introduce a statistical procedure based on multinomial logistic regression analysis for such scenarios, including variable screening, model selection, order selection for response categories, [...] Read more.
Categorical data analysis becomes challenging when high-dimensional sparse covariates are involved, which is often the case for omics data. We introduce a statistical procedure based on multinomial logistic regression analysis for such scenarios, including variable screening, model selection, order selection for response categories, and variable selection. We perform our procedure on high-dimensional gene expression data with 801 patients, 2426 genes, and five types of cancerous tumors. As a result, we recommend three finalized models: one with 74 genes achieves extremely low cross-entropy loss and zero predictive error rate based on a five-fold cross-validation; and two other models with 31 and 4 genes, respectively, are recommended for prognostic multi-gene signatures. Full article
14 pages, 291 KiB  
Article
Evolved Eugenics and Reinforcement of “Othering”: Renewed Ethico-Legal Perspectives of Genome Editing in Reproduction
by Pin Lean Lau
BioTech 2023, 12(3), 51; https://doi.org/10.3390/biotech12030051 - 11 Jul 2023
Cited by 1 | Viewed by 2742
Abstract
This article extends an exploration into renewed ethico-legal perspectives of genome editing technologies, examined from an evolved conceptualization of eugenics in contemporary human reproduction. Whilst the ethico-legal conundrums presented by genome-editing technologies in various aspects of modern medicine have thus far inspired a [...] Read more.
This article extends an exploration into renewed ethico-legal perspectives of genome editing technologies, examined from an evolved conceptualization of eugenics in contemporary human reproduction. Whilst the ethico-legal conundrums presented by genome-editing technologies in various aspects of modern medicine have thus far inspired a comprehensive trove of academic scholarship—and notwithstanding the World Health Organization’s (WHO) publication of guidelines on human genome editing in 2021—the legislative landscape for these technologies remain relatively unchanged. Accordingly, this paper presents the unresolved problematic questions that still require significant reflection. First, the paper highlights these questions, which primarily center around the tension between reproductive autonomy and the legal governance of reproductive/genome editing technologies by a democratic state. Secondly, the paper interrogates the evolved conceptualization of eugenics, exercised on the part of prospective parents as part of reproductive autonomy. By this, the paper predicates that it indirectly reinforces societal and systemic problems of discrimination and “othering”, increasing reproductive inequalities in excluded communities. Thirdly, the paper attempts to offer narratives of intersectionality as a facilitating tool in a continuing dialogue to build belonging, foster a healthy and balanced exercise of reproductive autonomy, and increase reproductive equalities. Full article
(This article belongs to the Special Issue Biotechnology and Bioethics)
15 pages, 3776 KiB  
Article
Novel Highly Efficient Antibacterial Chitosan-Based Films
by Omar M. Khubiev, Anton R. Egorov, Nikolai N. Lobanov, Elena A. Fortalnova, Anatoly A. Kirichuk, Alexander G. Tskhovrebov and Andreii S. Kritchenkov
BioTech 2023, 12(3), 50; https://doi.org/10.3390/biotech12030050 - 07 Jul 2023
Cited by 1 | Viewed by 1894
Abstract
In this study, we elaborated new chitosan-based films reinforced by iron(III)-containing chitosan nanoparticles Fe(III)-CS-NPs at different concentrations. We found that the optimum concentration of Fe(III)-CS-NPs for the improvement of antibacterial and mechanical properties of the films was 10% (σb = ca. 8.8 [...] Read more.
In this study, we elaborated new chitosan-based films reinforced by iron(III)-containing chitosan nanoparticles Fe(III)-CS-NPs at different concentrations. We found that the optimum concentration of Fe(III)-CS-NPs for the improvement of antibacterial and mechanical properties of the films was 10% (σb = ca. 8.8 N/mm2, εb = ca. 41%, inhibition zone for S. aureus = ca. 16.8 mm and for E. coli = ca. 11.2 mm). Also, using the click-chemistry approach (thiol–ene reaction), we have synthesized a novel water-soluble cationic derivative of chitin. The addition of this derivative of chitin to the chitosan polymer matrix of the elaborated film significantly improved its mechanical (σb = ca. 11.6 N/mm2, εb = ca. 75%) and antimicrobial (inhibition zone for S. aureus = ca. 19.6 mm and for E. coli = ca. 14.2 mm) properties. The key mechanism of the antibacterial action of the obtained films is the disruption of the membranes of bacterial cells. The elaborated antibacterial films are of interest for potential biomedical and food applications. Full article
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16 pages, 1241 KiB  
Article
Co-Producing Phycocyanin and Bioplastic in Arthrospira platensis Using Carbon-Rich Wastewater
by Hajar Shayesteh, Damian W. Laird, Leonie J. Hughes, Mohammad A. Nematollahi, Amin Mirshamsi Kakhki and Navid R. Moheimani
BioTech 2023, 12(3), 49; https://doi.org/10.3390/biotech12030049 - 03 Jul 2023
Cited by 1 | Viewed by 2245
Abstract
Microalgae can treat waste streams containing elevated levels of organic carbon and nitrogen. This process can be economically attractive if high value products are created simultaneously from the relatively low-cost waste stream. Co-production of two high value microalgal products, phycocyanin and polyhydroxybutyrate (PHB), [...] Read more.
Microalgae can treat waste streams containing elevated levels of organic carbon and nitrogen. This process can be economically attractive if high value products are created simultaneously from the relatively low-cost waste stream. Co-production of two high value microalgal products, phycocyanin and polyhydroxybutyrate (PHB), was investigated using non-axenic Arthrospira platensis MUR126 and supplemental organic carbon (acetate, oxalate, glycerol and combinations). All supplemented cultures had higher biomass yield (g/L) than photoautotrophic control. All cultures produced PHB (3.6–7.8% w/w), except the control and those fed oxalate. Supplemented cultures showed a two to three-fold increase in phycocyanin content over the eight-day cultivation. Results indicate co-production of phycocyanin and PHB is possible in A. platensis, using mixed-waste organic carbon. However, supplementation resulted in growth of extremophile bacteria, particularly in cultures fed glycerol, and this had a negative impact on culture health. Refinement of the carbon dosing rate is required to minimise impacts of native bacterial contamination. Full article
(This article belongs to the Special Issue Interaction between Microalgae and Light: Biotechnological Insights)
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