BioTech

14 pages, 3325 KiB

Open AccessArticle

Principle Investigation and Method Standardization of Inhibition Zone Assay Based on Antimicrobial Peptides Extracted from Black Soldier Fly Larvae

by Wenyue Shen, Ranxia Xue, Yanxia Liu, Shibo Sun, Xi Chen, Dongye Sun, Han Ouyang, Yuxin Li, Jianqiang Xu, Xiaoying Dong, Fengyun Ji and Weiping Xu

BioTech 2024, 13(3), 31; https://doi.org/10.3390/biotech13030031 - 9 Aug 2024

Viewed by 459

Abstract

The black soldier fly is a valuable resource insect capable of transforming organic waste while producing antimicrobial peptides (AMPs). The inhibition zone assay (IZA) is a method used to demonstrate the antimicrobial activity of AMPs. This study aimed to examine the experimental principles [...] Read more.

The black soldier fly is a valuable resource insect capable of transforming organic waste while producing antimicrobial peptides (AMPs). The inhibition zone assay (IZA) is a method used to demonstrate the antimicrobial activity of AMPs. This study aimed to examine the experimental principles and establish a standardized IZA method. Results indicated that the AMPs extract consisted of proteins ranging in molecular weights from 0 to 40 kDa. The AMPs diffused radially on an agar plate through an Oxford cup. The diffusion radius was influenced by the concentration and volume of the AMPs but ultimately determined by the mass of the AMPs. The swabbing method was found to be effective for inoculating bacteria on the agar plate. Among the conditions tested, the plate nutrient concentration was the most sensitive factor for the IZA, followed by bacterial concentration and incubation time. Optimal conditions for the IZA included a nutrient plate of 0.5× TSA, a bacterial concentration of 10⁶ CFU/mL, and an incubation time of 12 h, with oxytetracycline (OTC) at 0.01 mg/mL serving as the positive control. The antimicrobial-specific activity of AMPs could be standardized by the ratio of inhibition zone diameters between AMPs and OTC. These findings contribute to the standardization of the IZA method for profiling the antimicrobial activity of AMPs. Full article

► Show Figures

Graphical abstract

22 pages, 3649 KiB

Open AccessArticle

CleanUpRNAseq: An R/Bioconductor Package for Detecting and Correcting DNA Contamination in RNA-Seq Data

by Haibo Liu, Kai Hu, Kevin O’Connor, Michelle A. Kelliher and Lihua Julie Zhu

BioTech 2024, 13(3), 30; https://doi.org/10.3390/biotech13030030 - 3 Aug 2024

Viewed by 536

Abstract

RNA sequencing (RNA-seq) has become a standard method for profiling gene expression, yet genomic DNA (gDNA) contamination carried over to the sequencing library poses a significant challenge to data integrity. Detecting and correcting this contamination is vital for accurate downstream analyses. Particularly, when [...] Read more.

RNA sequencing (RNA-seq) has become a standard method for profiling gene expression, yet genomic DNA (gDNA) contamination carried over to the sequencing library poses a significant challenge to data integrity. Detecting and correcting this contamination is vital for accurate downstream analyses. Particularly, when RNA samples are scarce and invaluable, it becomes essential not only to identify but also to correct gDNA contamination to maximize the data’s utility. However, existing tools capable of correcting gDNA contamination are limited and lack thorough evaluation. To fill the gap, we developed CleanUpRNAseq, which offers a comprehensive set of functionalities for identifying and correcting gDNA-contaminated RNA-seq data. Our package offers three correction methods for unstranded RNA-seq data and a dedicated approach for stranded data. Through rigorous validation on published RNA-seq datasets with known levels of gDNA contamination and real-world RNA-seq data, we demonstrate CleanUpRNAseq’s efficacy in detecting and correcting detrimental levels of gDNA contamination across diverse library protocols. CleanUpRNAseq thus serves as a valuable tool for post-alignment quality assessment of RNA-seq data and should be integrated into routine workflows for RNA-seq data analysis. Its incorporation into OneStopRNAseq should significantly bolster the accuracy of gene expression quantification and differential expression analysis of RNA-seq data. Full article

(This article belongs to the Section Computational Biology)

► Show Figures

Figure 1

14 pages, 2770 KiB

Open AccessArticle

Molecular Insight into the Response of Lactic Acid Bacteria to Bile Acids

by Caren N. Moreno, Jorge N. Gomez, María P. Taranto, Ana E. Ledesma and Ana Y. Bustos

BioTech 2024, 13(3), 29; https://doi.org/10.3390/biotech13030029 - 2 Aug 2024

Viewed by 439

Abstract

Bile acids (BAs) are the main endogenous modulators of the composition and metabolic activity of the intestinal microbiota. In the present work, the effect of conjugated (glycodeoxycholic, glycocholic, taurodeoxycholic, taurocholic acids) and free BAs [cholic acid (CA) and deoxycholic acid (DCA)] on the [...] Read more.

Bile acids (BAs) are the main endogenous modulators of the composition and metabolic activity of the intestinal microbiota. In the present work, the effect of conjugated (glycodeoxycholic, glycocholic, taurodeoxycholic, taurocholic acids) and free BAs [cholic acid (CA) and deoxycholic acid (DCA)] on the survival, biological molecules, and structural and surface properties of two potential probiotic lactic acid bacteria (LAB) was evaluated. For this, viability assays, Raman spectroscopy, scanning electron microscopy (SEM), and zeta potential (ZP) measurements were employed. Our results evidenced that free BAs were more toxic than conjugates, with CA being significantly more harmful than deoxycholic acid (DCA). RAMAN studies show that BAs modify the bands corresponding to proteins, lipids, carbohydrates, and DNA. SEM showed that BAs cause surface distortions with depressions and fold formation, as well as incomplete cell division. DCA was the one that least altered the ZP of bacteria when compared to CA and taurodeoxycholic acid, with gradual changes towards more positive values. In general, the magnitude of these effects was different according to the BA and its concentration, being more evident in the presence of CA, even at low concentrations, which would explain its greater inhibitory effect. This work provides solid evidence on the effects of BAs on LAB that will allow for the development of strategies by which to modulate the composition of the microbiota positively. Full article

(This article belongs to the Section Agricultural and Food Biotechnology)

► Show Figures

Figure 1

14 pages, 1611 KiB

Open AccessArticle

Removal of Cadmium (II) from Aqueous Solution Using Galdieria sulphuraria CCMEE 5587.1

by Hari Lal Kharel, Lina Jha, Melissa Tan and Thinesh Selvaratnam

BioTech 2024, 13(3), 28; https://doi.org/10.3390/biotech13030028 - 1 Aug 2024

Viewed by 322

Abstract

The release of cadmium into the environment is a significant global concern due to its toxicity, non-biodegradability, and persistence in nature. There is an urgent need for effective, eco-friendly, and cost-effective systems for removing Cd because of the many drawbacks of conventional physicochemical [...] Read more.

The release of cadmium into the environment is a significant global concern due to its toxicity, non-biodegradability, and persistence in nature. There is an urgent need for effective, eco-friendly, and cost-effective systems for removing Cd because of the many drawbacks of conventional physicochemical techniques. This study investigated the ability of the extremophile red microalgal strain Galdieria sulphuraria CCMEE 5587.1 to tolerate and remove Cd (II) ions at acidic pH in a controlled laboratory environment. Three distinct concentrations of Cd (1.5 mg L⁻¹, 3 mg L⁻¹, and 6 mg L⁻¹) were introduced to the cyanidium medium, and G. sulphuraria cells were introduced in the medium and grown for ten days. Four distinct aspects were identified regarding Cd removal: time course Cd removal, total Cd removal, extracellular Cd removal, and intracellular Cd removal. The inhibitory effects of Cd on G. sulphuraria growth were observed using a daily growth profile. Initial incubation days showed an inhibition of G. sulphuraria growth. In addition, increasing the Cd concentration in the medium decreased the growth rate of G. sulphuraria. Rapid Cd removal occurred on the first day of the experiment, followed by a steady removal of Cd until the last day. The highest total removal efficiency occurred in a medium containing 3 mg L⁻¹ of Cd ions, which was 30%. In contrast, the highest sorption capacity occurred in a medium containing 6 mg L⁻¹ of Cd ions, which was 1.59 mg g⁻¹ of dry biomass. In all media compositions, a major fraction (>80%) of Cd removal occurred via adsorption on the cell surface (extracellular). These results showed that G. sulphuraria cells can remove Cd ions from aqueous solution, which makes them a potential bioremediation option for heavy metal removal. Full article

(This article belongs to the Section Environmental Biotechnology)

► Show Figures

Figure 1

31 pages, 2340 KiB

Open AccessFeature PaperReview

Hydroponics with Microalgae and Cyanobacteria: Emerging Trends and Opportunities in Modern Agriculture

by Prabhaharan Renganathan, Edgar Omar Rueda Puente, Natalia V. Sukhanova and Lira A. Gaysina

BioTech 2024, 13(3), 27; https://doi.org/10.3390/biotech13030027 - 22 Jul 2024

Viewed by 979

Abstract

The global population is expected to reach 9.5 billion, which means that crop productivity needs to double to meet the growing population’s food demand. Soil degradation and environmental factors, such as climate events, significantly threaten crop production and global food security. Furthermore, rapid [...] Read more.

The global population is expected to reach 9.5 billion, which means that crop productivity needs to double to meet the growing population’s food demand. Soil degradation and environmental factors, such as climate events, significantly threaten crop production and global food security. Furthermore, rapid urbanization has led to 55% of the world’s population migrating to cities, and this proportion is expected to increase to 75% by 2050, which presents significant challenges in producing staple foods through conventional hinterland farming. Numerous studies have proposed various sustainable farming techniques to combat the shortage of farmable land and increase food security in urban areas. Soilless farming techniques such as hydroponics have gained worldwide popularity due to their resource efficiency and production of superior-quality fresh products. However, using chemical nutrients in a conventional hydroponic system can have significant environmental impacts, including eutrophication and resource depletion. Incorporating microalgae into hydroponic systems as biostimulants offers a sustainable and ecofriendly approach toward circular bioeconomy strategies. The present review summarizes the plant growth-promoting activity of microalgae as biostimulants and their mechanisms of action. We discuss their effects on plant growth parameters under different applications, emphasizing the significance of integrating microalgae into a closed-loop circular economy model to sustainably meet global food demands. Full article

(This article belongs to the Topic Microbial Biotechnology Products and Biocatalysis Processes for a Sustainable Bioeconomy)

► Show Figures

Figure 1

14 pages, 8510 KiB

Open AccessArticle

Strategies for Increasing the Throughput of Genetic Screening: Lessons Learned from the COVID-19 Pandemic within a University Community

by Fernanda Miguel, A. Raquel Baleizão, A. Gabriela Gomes, Helena Caria, Fátima N. Serralha and Marta C. Justino

BioTech 2024, 13(3), 26; https://doi.org/10.3390/biotech13030026 - 11 Jul 2024

Viewed by 751

Abstract

Amidst the COVID-19 pandemic, the Polytechnic University of Setúbal (IPS) used its expertise in molecular genetics to establish a COVID-19 laboratory, addressing the demand for community-wide testing. Following standard protocols, the IPS COVID Lab received national accreditation in October 2020 and was registered [...] Read more.

Amidst the COVID-19 pandemic, the Polytechnic University of Setúbal (IPS) used its expertise in molecular genetics to establish a COVID-19 laboratory, addressing the demand for community-wide testing. Following standard protocols, the IPS COVID Lab received national accreditation in October 2020 and was registered in February 2021. With the emergence of new SARS-CoV-2 variants and safety concerns for students and staff, the lab was further challenged to develop rapid and sensitive diagnostic technologies. Methodologies such as sample-pooling extraction and multiplex protocols were developed to enhance testing efficiency without compromising accuracy. Through Real-Time Reverse Transcription Polymerase Chain Reaction (RT-qPCR) analysis, the effectiveness of sample pooling was validated, proving to be a clear success in COVID-19 screening. Regarding multiplex analysis, the IPS COVID Lab developed an in-house protocol, achieving a sensitivity comparable to that of standard methods while reducing operational time and reagent consumption. This approach, requiring only two wells of a PCR plate (instead of three for samples), presents a more efficient alternative for future testing scenarios, increasing its throughput and testing capacity while upholding accuracy standards. The lessons learned during the SARS-CoV-2 pandemic provide added value for future pandemic situations. Full article

(This article belongs to the Section Medical Biotechnology)

► Show Figures

Graphical abstract

14 pages, 2537 KiB

Open AccessArticle

An Efficient and Rapid Protocol for Somatic Shoot Organogenesis from Juvenile Hypocotyl-Derived Callus of Castor Bean cv. Zanzibar Green

by Danaya V. Demidenko, Nataliya V. Varlamova, Taisiya M. Soboleva, Aleksandra V. Shitikova and Marat R. Khaliluev

BioTech 2024, 13(3), 25; https://doi.org/10.3390/biotech13030025 - 4 Jul 2024

Viewed by 452

Abstract

Aseptic seedlings of different ages derived from surface-sterilized mature seeds were applied as an explant source. Various explants such as 7- and 21-day-old hypocotyl fragments, 42-day-old nodal stem segments, and transverse nodal segments of stem, as well as leaf petioles, were cultured on [...] Read more.

Aseptic seedlings of different ages derived from surface-sterilized mature seeds were applied as an explant source. Various explants such as 7- and 21-day-old hypocotyl fragments, 42-day-old nodal stem segments, and transverse nodal segments of stem, as well as leaf petioles, were cultured on the agar-solidified Murashige and Skoog (MS) basal medium supplemented with 0.1 mg/L IAA, 5 mg/L AgNO₃ and different types and concentrations of cytokinin (1 mg/L zeatin, 0.25 mg/L thidiazuron (TDZ), and 5 mg/L 6-benzylaminopurine (6-BAP)). Consequently, it was found that 7- and 21-day-old hypocotyl fragments, as well as nodal stem segments obtained from adult aseptic seedlings, are characterized by a high explant viability and callus formation capacity with a frequency of 79.7–100%. However, the success of in vitro somatic shoot organogenesis was significantly determined not only by the culture medium composition and explant type but also depending on its age, as well as on the size and explant preparation in cases of hypocotyl and age-matched nodal stem fragments, respectively. Multiple somatic shoot organogenesis (5.7 regenerants per explant) with a frequency of 67.5% was achieved during 3 subcultures of juvenile hypocotyl-derived callus tissue on MS culture medium containing 0.25 mg/L TDZ as cytokinin source. Castor bean regenerants were excised from the callus and successfully rooted on ½ MS basal medium without exogenous auxin (81%). In vitro plantlets with well-developed roots were adapted to ex vitro conditions with a frequency of 90%. Full article

(This article belongs to the Section Agricultural and Food Biotechnology)

► Show Figures

Figure 1

13 pages, 2322 KiB

Open AccessArticle

In Vitro: The Extraordinary Enhancement in Rutin Accumulation and Antioxidant Activity in Philodendron “Imperial Red” Plantlets Using Ti-Mo-Ni-O Nanotubes as a Novel Elicitor

by Hanan S. Ebrahim, Nourhan M. Deyab, Basamat S. Shaheen, Ahmed M. M. Gabr and Nageh K. Allam

BioTech 2024, 13(3), 24; https://doi.org/10.3390/biotech13030024 - 4 Jul 2024

Viewed by 655

Abstract

Rutin, a flavonoid phytochemical compound, plays a vital role in human health. It is used in treating capillary fragility and has anti-Alzheimer, anti-inflammatory, and antioxidant effects. In this study, Ti-Mo-Ni-O nanotubes (NTs) were used, for the first time, in an unprecedented plant biotechnology [...] Read more.

Rutin, a flavonoid phytochemical compound, plays a vital role in human health. It is used in treating capillary fragility and has anti-Alzheimer, anti-inflammatory, and antioxidant effects. In this study, Ti-Mo-Ni-O nanotubes (NTs) were used, for the first time, in an unprecedented plant biotechnology application, wherein in vitro Philodendron shoots (Philodendron erubescens) known as “Imperial Red” were targeted for rutin accumulation. The antioxidant responses and the accumulation of rutin were evaluated in treated Philodendron erubescens (P. erubescens) shoots using 5.0 mg/L of Ti-Mo-Ni-O NTs. The total phenolic content and total flavonoid content were estimated, and an ABTS⁺ assay, FRAP assay, and iron metal chelation assay were performed. The application of Ti-Mo-Ni-O NTs enhanced the rutin content considerably from 0.02 mg/g to 2.96 mg/g for dry-weight shootlet extracts. Therefore, the use of Ti-Mo-Ni-O NTs is proposed to be a superior alternative to elevate the rutin content. The aim of the current study is to target P. erubescens shoots grown in vitro for the accumulation of rutin compounds using Ti-Mo-Ni-O NT powder, to determine the quantitative and qualitative accumulation of rutin via HPLC–DAD analysis, and to estimate the antioxidant activity of P. erubescens shoot extract. This study presents a novel methodology for utilizing nano-biotechnology in the synthesis of plant secondary metabolites. Full article

► Show Figures

Figure 1

15 pages, 2031 KiB

Open AccessArticle

Systemic Effects of Photoactivated 5,10,15,20-tetrakis(N-methylpyridinium-3-yl) Porphyrin on Healthy Drosophila melanogaster

by Ana Filošević Vujnović, Sara Čabrijan, Martina Mušković, Nela Malatesti and Rozi Andretić Waldowski

BioTech 2024, 13(3), 23; https://doi.org/10.3390/biotech13030023 - 3 Jul 2024

Viewed by 551

Abstract

Porphyrins are frequently employed in photodynamic therapy (PDT), a non-invasive technique primarily utilized to treat subcutaneous cancers, as photosensitizing agents (PAs). The development of a new PA with improved tissue selectivity and efficacy is crucial for expanding the application of PDT for the [...] Read more.

Porphyrins are frequently employed in photodynamic therapy (PDT), a non-invasive technique primarily utilized to treat subcutaneous cancers, as photosensitizing agents (PAs). The development of a new PA with improved tissue selectivity and efficacy is crucial for expanding the application of PDT for the management of diverse cancers. We investigated the systemic effects of 5,10,15,20-tetrakis(N-methylpyridinium-3-yl)-porphyrin (TMPyP3) using Drosophila melanogaster adult males. We established the oral administration schedule and demonstrated that TMPyP3 was absorbed and stored higher in neuronal than in non-neuronal extracts. Twenty-four hours after oral TMPyP3 photoactivation, the quantity of hydrogen peroxide (H₂O₂) increased, but exclusively in the head extracts. Regardless of photoactivation, TMPyP3 resulted in a reduced concentration of H₂O₂ after 7 days, and this was linked with a decreased capacity to climb, as indicated by negative geotaxis. The findings imply that systemic TMPyP3 therapy may disrupt redox regulation, impairing cellular signaling and behavioral outcomes in the process. To determine the disruptive effect of porphyrins on redox homeostasis, its duration, and the mechanistic variations in retention across various tissues, more research is required. Full article

(This article belongs to the Section Medical Biotechnology)

► Show Figures

Figure 1

14 pages, 2059 KiB

Open AccessArticle

A Machine Learning-Based Web Tool for the Severity Prediction of COVID-19

by Avgi Christodoulou, Martha-Spyridoula Katsarou, Christina Emmanouil, Marios Gavrielatos, Dimitrios Georgiou, Annia Tsolakou, Maria Papasavva, Vasiliki Economou, Vasiliki Nanou, Ioannis Nikolopoulos, Maria Daganou, Aikaterini Argyraki, Evaggelos Stefanidis, Gerasimos Metaxas, Emmanouil Panagiotou, Ioannis Michalopoulos and Nikolaos Drakoulis

BioTech 2024, 13(3), 22; https://doi.org/10.3390/biotech13030022 - 1 Jul 2024

Cited by 1 | Viewed by 990

Abstract

Predictive tools provide a unique opportunity to explain the observed differences in outcome between patients of the COVID-19 pandemic. The aim of this study was to associate individual demographic and clinical characteristics with disease severity in COVID-19 patients and to highlight the importance [...] Read more.

Predictive tools provide a unique opportunity to explain the observed differences in outcome between patients of the COVID-19 pandemic. The aim of this study was to associate individual demographic and clinical characteristics with disease severity in COVID-19 patients and to highlight the importance of machine learning (ML) in disease prognosis. The study enrolled 344 unvaccinated patients with confirmed SARS-CoV-2 infection. Data collected by integrating questionnaires and medical records were imported into various classification machine learning algorithms, and the algorithm and the hyperparameters with the greatest predictive ability were selected for use in a disease outcome prediction web tool. Of 111 independent features, age, sex, hypertension, obesity, and cancer comorbidity were found to be associated with severe COVID-19. Our prognostic tool can contribute to a successful therapeutic approach via personalized treatment. Although at the present time vaccination is not considered mandatory, this algorithm could encourage vulnerable groups to be vaccinated. Full article

(This article belongs to the Topic Advances in Bioinformatics and Computational Biology of Human Disease)

► Show Figures

Figure 1

12 pages, 1661 KiB

Open AccessArticle

Influence of Critical Parameters on the Extraction of Concentrated C-PE from Thermotolerant Cyanobacteria

by Ariadna H. Vergel-Suarez, Janet B. García-Martínez, German L. López-Barrera, Néstor A. Urbina-Suarez and Andrés F. Barajas-Solano

BioTech 2024, 13(3), 21; https://doi.org/10.3390/biotech13030021 - 24 Jun 2024

Viewed by 694

Abstract

This work aimed to identify the influence of pH, molarity, w/v fraction, extraction time, agitation, and either a sodium (Na₂HPO₄·7H₂O-NaH₂PO₄·H₂O) or potassium buffer (K₂HPO₄-KH₂ [...] Read more.

This work aimed to identify the influence of pH, molarity, w/v fraction, extraction time, agitation, and either a sodium (Na₂HPO₄·7H₂O-NaH₂PO₄·H₂O) or potassium buffer (K₂HPO₄-KH₂PO₄) used in the extraction of C-phycoerythrin (C-PE) from a thermotolerant strain of Potamosiphon sp. An experimental design (Minimum Run Resolution V Factorial Design) and a Central Composite Design (CCD) were used. According to the statistical results of the first design, the K-PO₄ buffer, pH, molarity, and w/v fraction are vital factors that enhance the extractability of C-PE. The construction of a CCD design of the experiments suggests that the potassium phosphate buffer at pH 5.8, longer extraction times (50 min), and minimal extraction speed (1000 rpm) are ideal for maximizing C-PE concentration, while purity is unaffected by the design conditions. This optimization improves extraction yields and maintains the desired bright purple color of the phycobiliprotein. Full article

(This article belongs to the Topic Microbial Biotechnology Products and Biocatalysis Processes for a Sustainable Bioeconomy)

► Show Figures

Figure 1

Journal Menu

Journal Browser

BioTech, Volume 13, Issue 3 (September 2024) – 11 articles

Further Information

Guidelines

MDPI Initiatives

Follow MDPI