BioTech

20 pages, 1727 KiB

Open AccessReview

Developments in Extracellular Matrix-Based Angiogenesis Therapy for Ischemic Heart Disease: A Review of Current Strategies, Methodologies and Future Directions

by Jad Hamze, Mark Broadwin, Christopher Stone, Kelsey C. Muir, Frank W. Sellke and M. Ruhul Abid

BioTech 2025, 14(1), 23; https://doi.org/10.3390/biotech14010023 - 19 Mar 2025

Viewed by 346

Abstract

Ischemic heart disease (IHD) is the leading cause of mortality worldwide, underscoring the urgent need for innovative therapeutic strategies. The cardiac extracellular matrix (ECM) undergoes extreme transformations during IHD, adversely influencing the heart’s structure, mechanics, and cellular signaling. Researchers investigating the regenerative capacity [...] Read more.

Ischemic heart disease (IHD) is the leading cause of mortality worldwide, underscoring the urgent need for innovative therapeutic strategies. The cardiac extracellular matrix (ECM) undergoes extreme transformations during IHD, adversely influencing the heart’s structure, mechanics, and cellular signaling. Researchers investigating the regenerative capacity of the diseased heart have turned their attention to exploring the modulation of ECM to improve therapeutic outcomes. In this review, we thoroughly examine the current state of knowledge regarding the cardiac ECM and its therapeutic potential in the ischemic myocardium. We begin by providing an overview of the fundamentals of cardiac ECM, focusing on the structural, functional, and regulatory mechanisms that drive its modulation. Subsequently, we examine the ECM’s interactions within both chronically ischemic and acutely infarcted myocardium, emphasizing key ECM components and their roles in modulating angiogenesis. Finally, we discuss recent ECM-based approaches in biomedical engineering, focusing on different types of scaffolds as delivery tools and their compositions, and conclude with future directions for therapeutic research. By harnessing the potential of these emerging ECM-based therapies, we aim to contribute to the development of novel therapeutic modalities for IHD. Full article

(This article belongs to the Section Medical Biotechnology)

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16 pages, 1473 KiB

Open AccessArticle

Identifying Antimicrobial Agents from Chlorella sorokiniana: A Biotechnological Approach Utilizing Eco-Friendly Extraction and Characterization Methods

by Elia Lio, Martina Dramis, Gianluca Ottolina and Francesco Secundo

BioTech 2025, 14(1), 22; https://doi.org/10.3390/biotech14010022 - 18 Mar 2025

Viewed by 305

Abstract

Natural compounds are increasingly favored over synthetic ones for their lower environmental impact. However, extraction and characterization processes typically rely on harsh conditions and conventional solvents, which are unsustainable and cause pollution. This study aimed to develop an eco-friendly extraction method to isolate [...] Read more.

Natural compounds are increasingly favored over synthetic ones for their lower environmental impact. However, extraction and characterization processes typically rely on harsh conditions and conventional solvents, which are unsustainable and cause pollution. This study aimed to develop an eco-friendly extraction method to isolate and evaluate the antimicrobial properties of bioactive compounds from Chlorella sorokiniana. Using dimethyl carbonate (DMC), methoxycyclopentane (CPME), and butan-2-one (MEK) as green solvents alongside chloroform as a non-green reference solvent, on both untreated and sodium hydroxide pre-treated microalgae biomass, extract yields of up to 182 ± 27 mg/g DW were obtained using MEK. Extracts from untreated microalgae biomass exhibited lower MIC values compared to those obtained with the same solvent from pre-treated biomass, when tested as antimicrobial agents against Escherichia coli, Bacillus megaterium, and Bacillus subtilis. The lowest MIC value (4.89 ± 0.05 µg/mL) was observed against E. coli using the extract from the untreated microalgae biomass with CPME, which was comparable to the vancomycin control (1.55 ± 0.03 µg/mL). Principal component analysis highlighted correlations between GC-MS-identified compounds and antimicrobial activity. ANOVA and post hoc tests (p < 0.05) confirmed solvent choice, and pre-treatment influenced yield and bioactivity. The results underscore green solvents as sustainable alternatives for extracting bioactive compounds from autotrophic microalgae. Full article

(This article belongs to the Section Industry, Agriculture and Food Biotechnology)

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17 pages, 825 KiB

Open AccessArticle

Genomic Characterization of Extremely Antibiotic-Resistant Strains of Pseudomonas aeruginosa Isolated from Patients of a Clinic in Sincelejo, Colombia

by Nerlis Pajaro-Castro, Erick Diaz-Morales and Kenia Hoyos

BioTech 2025, 14(1), 21; https://doi.org/10.3390/biotech14010021 - 16 Mar 2025

Viewed by 340

Abstract

Pseudomonas aeruginosa is an opportunistic pathogen classified as a priority and a great public health concern; therefore, this research focuses on the genomic characterization of extremely resistant strains of P. aeruginosa isolated from patients in a clinic in Sincelejo, Colombia. Seven strains were [...] Read more.

Pseudomonas aeruginosa is an opportunistic pathogen classified as a priority and a great public health concern; therefore, this research focuses on the genomic characterization of extremely resistant strains of P. aeruginosa isolated from patients in a clinic in Sincelejo, Colombia. Seven strains were analyzed by whole genome sequencing using the Illumina NovaSeq platform, with a focus on the identification of resistance genes and virulence factors through the CARD and VFDB databases. An ANI (Average Nucleotide Identity) analysis was carried out to determine the genetic relationship between the strains, complemented by a phylogenomic analysis to place the strains in different evolutionary clades. The results revealed that six of the strains are of Colombian origin, while one strain (547256) belongs to the high-risk clone ST773, previously unidentified in Colombia. Genome size ranged from 6 to 7.4 Mbp, indicating differences in genetic content among strains. Phylogenomic analysis confirmed that five strains belong to a multidrug-resistant (MDR) group, while one strain (572897) showed high alignment with a laboratory strain, and strain 547256 was not associated with any specific clade. Clinically, 100% of strains showed carbapenem resistance, resistance genes, and virulence factors that make them difficult to treat. This study provides key insights into the genetic diversity and resistance patterns of P. aeruginosa in this region, underscoring the need to monitor high-risk clones and optimize therapeutic strategies. Full article

(This article belongs to the Section Computational Biology)

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13 pages, 3304 KiB

Open AccessArticle

Using Nano-Luciferase Binary (NanoBiT) Technology to Assess the Interaction Between Viral Spike Protein and Angiotensin-Converting Enzyme II by Aptamers

by Meng-Wei Lin, Cheng-Han Lin, Hua-Hsin Chiang, Irwin A. Quintela, Vivian C. H. Wu and Chih-Sheng Lin

BioTech 2025, 14(1), 20; https://doi.org/10.3390/biotech14010020 - 15 Mar 2025

Viewed by 471

Abstract

Nano-luciferase binary technology (NanoBiT)-based pseudoviral sensors are innovative tools for monitoring viral infection dynamics. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects host cells via its trimeric surface spike protein, which binds to the human angiotensin-converting enzyme II (hACE2) receptor. This interaction is [...] Read more.

Nano-luciferase binary technology (NanoBiT)-based pseudoviral sensors are innovative tools for monitoring viral infection dynamics. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects host cells via its trimeric surface spike protein, which binds to the human angiotensin-converting enzyme II (hACE2) receptor. This interaction is crucial for viral entry and serves as a key target for therapeutic interventions against coronavirus disease 2019 (COVID-19). Aptamers, short single-stranded DNA (ssDNA) or RNA molecules, are highly specific, high-affinity biorecognition elements for detecting infective pathogens. Despite their potential, optimizing viral infection assays using traditional protein–protein interaction (PPI) methods often face challenges in optimizing viral infection assays. In this study, we selected and evaluated aptamers for their ability to interact with viral proteins, enabling the dynamic visualization of infection progression. The NanoBiT-based pseudoviral sensor demonstrated a rapid increase in luminescence within 3 h, offering a real-time measure of viral infection. A comparison of detection technologies, including green fluorescent protein (GFP), luciferase, and NanoBiT technologies for detecting PPI between the pseudoviral spike protein and hACE2, highlighted NanoBiT’s superior sensitivity and performance, particularly in aptamer selection. This bioluminescent system provides a robust, sensitive, and early-stage quantitative approach to studying viral infection dynamics. Full article

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17 pages, 608 KiB

Open AccessArticle

A Coupled Model of the Cardiovascular and Immune Systems to Analyze the Effects of COVID-19 Infection

by Camila Ribeiro Passos, Alexandre Altamir Moreira, Ruy Freitas Reis, Rodrigo Weber dos Santos, Marcelo Lobosco and Bernardo Martins Rocha

BioTech 2025, 14(1), 19; https://doi.org/10.3390/biotech14010019 - 12 Mar 2025

Viewed by 496

Abstract

The COVID-19 pandemic has underscored the importance of understanding the interplay between the cardiovascular and immune systems during viral infections. SARS-CoV-2 enters human cells via the ACE-2 enzyme, initiating a cascade of immune responses. This study presents a coupled mathematical model that integrates [...] Read more.

The COVID-19 pandemic has underscored the importance of understanding the interplay between the cardiovascular and immune systems during viral infections. SARS-CoV-2 enters human cells via the ACE-2 enzyme, initiating a cascade of immune responses. This study presents a coupled mathematical model that integrates the cardiovascular system (CVS) and immune system (IS), capturing their complex interactions during infection. The CVS model, based on ordinary differential equations, describes heart dynamics and pulmonary and systemic circulation, while the IS model simulates immune responses to SARS-CoV-2, including immune cell interactions and cytokine production. A coupling strategy transfers information from the IS to the CVS at specific intervals, enabling the exploration of immune-driven cardiovascular effects. Numerical simulations examined how these interactions influence infection severity and recovery. The coupled model accurately replicated the evolution of cardiac function in survivors and non-survivors of COVID-19. Survivors exhibited a left ventricular ejection fraction (LVEF) reduction of up to

25 %

while remaining within normal limits, whereas non-survivors showed a severe 4-fold decline, indicative of myocardial dysfunction. Similarly, the right ventricular ejection fraction (RV EF) decreased by approximately

50 %

in survivors but underwent a drastic 5-fold reduction in non-survivors. These findings highlight the model’s capacity to distinguish differential cardiac dysfunction across clinical outcomes and its potential to enhance our understanding of COVID-19 pathophysiology. Full article

(This article belongs to the Section Computational Biology)

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14 pages, 3343 KiB

Open AccessArticle

Characterization of a GH43 Bifunctional Glycosidase from Endophytic Chaetomium globosum and Its Potential Application in the Biotransformation of Ginsenosides

by Yao Lu, Qiang Jiang, Yamin Dong, Runzhen Ji, Yiwen Xiao, Du Zhu and Boliang Gao

BioTech 2025, 14(1), 18; https://doi.org/10.3390/biotech14010018 - 12 Mar 2025

Viewed by 487

Abstract

The GH43 family of glycosidases represents an important class of industrial enzymes that are widely utilized across the food, pharmaceutical, and various other sectors. In this study, we identified a GH43 family glycoside hydrolytic enzyme, Xyaf313, derived from the plant endophytic fungus [...] Read more.

The GH43 family of glycosidases represents an important class of industrial enzymes that are widely utilized across the food, pharmaceutical, and various other sectors. In this study, we identified a GH43 family glycoside hydrolytic enzyme, Xyaf313, derived from the plant endophytic fungus Chaetomium globosum DX-THS3, which is capable of transforming several common ginsenosides. The enzyme function analysis reveals that Xyaf313 exhibits dual functionality, displaying both α-L-arabinofuranosidase and β-D-xylosidase activity. When acting as an α-L-arabinofuranosidase, Xyaf313 achieves optimal enzyme activity of 23.96 U/mg at a temperature of 50 °C and a pH of 7. In contrast, its β-D-xylosidase activity results in a slight reduction in enzyme activity to 23.24 U/mg, with similar optimal temperature and pH conditions to those observed for the α-L-arabinofuranosidase activity. Furthermore, Xyaf313 demonstrates considerable resistance to most metal ions and common chemical reagents. Notably, while the maximum enzyme activity of Xyaf313 occurs at 50 °C, it maintains high activity at room temperature (30 °C), with relative enzyme activity exceeding 90%. Measurements of ginsenoside transformation show that Xyaf313 can convert common ginsenosides Rc, Rb₁, Rb₂, and Rb₃ into Rd, underscoring its potential for pharmaceutical applications. Overall, our findings contribute to the identification of a new class of bifunctional GH43 glycoside hydrolases, highlight the significance of plant endophytic fungi as a promising resource for the screening of carbohydrate-decomposing enzymes, and present new candidate enzymes for the biotransformation of ginsenosides. Full article

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17 pages, 1553 KiB

Open AccessArticle

Chemical Profiling and Bioactivity of Microalgae Extracts for Enhancing Growth and Anthracnose Resistance in the Common Bean (Phaseolus vulgaris L.)

by Alessandro A. dos Santos, Camila Nader, Mateus B. de Freitas, César F. Ribeiro, Geovanna de Oliveira Costa, Louis P. Sandjo, Alex S. Poltronieri, Roberto B. Derner and Marciel J. Stadnik

BioTech 2025, 14(1), 17; https://doi.org/10.3390/biotech14010017 - 8 Mar 2025

Viewed by 508

Abstract

The present study aimed to chemically profile the hydroalcoholic extracts from the microalgae (MEs) Nannochloropsis oculata, Phaeodactylum tricornutum, Tetradesmus obliquus, and Tetraselmis tetrathele and evaluate their effects on the development of Colletotrichum lindemuthianum and anthracnose symptoms, as well as on the [...] Read more.

The present study aimed to chemically profile the hydroalcoholic extracts from the microalgae (MEs) Nannochloropsis oculata, Phaeodactylum tricornutum, Tetradesmus obliquus, and Tetraselmis tetrathele and evaluate their effects on the development of Colletotrichum lindemuthianum and anthracnose symptoms, as well as on the initial growth of bean plants. For this, MEs were analyzed using UPLC coupled with a mass spectrometer, allowing the identification of peaks and annotation of potential metabolites. Fungal mycelial growth was assessed seven days after inoculation, and conidial germination was measured 72 h after incubation, using ME concentrations of 0, 0.1, 0.5, and 1.0 mg·mL⁻¹. Bean seeds of the IPR Uirapuru cultivar were sown and treated with 3 mL of extracts at four time points: at sowing and 72 h after each previous treatment. After 11 days of cultivation in a growth chamber, the plants were divided into two groups: one for anthracnose control assessment and the other for evaluating growth promotion by MEs. Plant length as well as fresh and dry weights of shoots and roots were determined, leaf pigments were quantified, and anthracnose severity was assessed using a diagrammatic scale. The UPLC analysis identified 32 compounds in the extracts of the four microalgae, belonging to different chemical and functional groups, with lipids being the most significant fraction. The extracts exhibited variability and diversity in chemical composition depending on the microalgal species. MEs did not affect mycelial growth yet increased the germination of C. lindemuthianum conidia, regardless of the dose or species used. Anthracnose severity was not affected by the microalgae extracts. Regarding growth promotion, the extracts showed varying effects but generally increased shoot and root length, fresh biomass, and leaf pigment content. Full article

(This article belongs to the Section Industry, Agriculture and Food Biotechnology)

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10 pages, 1294 KiB

Open AccessCommunication

Towards a Survival-Based Cellular Assay for the Selection of Protease Inhibitors in Escherichia coli

by William Y. Oyadomari, Elizangela A. Carvalho, Gabriel E. Machado, Ana Júlia O. Machado, Gabriel S. Santos, Marcelo Marcondes and Vitor Oliveira

BioTech 2025, 14(1), 16; https://doi.org/10.3390/biotech14010016 - 7 Mar 2025

Viewed by 407

Abstract

We describe a method tailored to the in-cell selection of protease inhibitors. In this method, a target protease is co-expressed with a selective substrate, the product of which kills host cells. Therefore, the method can be applied to identify potential inhibitors based on [...] Read more.

We describe a method tailored to the in-cell selection of protease inhibitors. In this method, a target protease is co-expressed with a selective substrate, the product of which kills host cells. Therefore, the method can be applied to identify potential inhibitors based on cell host survival when inhibition of the target protease occurs. The TEV protease was chosen for this proof-of-concept experiment. The genetically encoded selective substrate is a single polypeptide chain composed of three parts: (1) a ccdB protein, which can cause host cell death when it accumulates inside the cell; (2) a protease cleavage sequence that can be changed according to the target protease, in this case the TEV substrate ENLYFQ↓G (↓-predicted cleavage site); and (3) the ssrA sequence (AANDENYALAA), which drives the polypeptide to degradation by the ClpX/ClpP complex inside host E. coli cells. In our experiment, co-expression of the active TEV protease and this selective substrate (ccdB-ENLYFQG-ssrA) caused the death of a significant host cell population, while control assays with an inactive mutant TEV Asp81Asn did not. Details of the methodology used are given, providing the basis for the application of similar systems for other proteases of interest. Full article

(This article belongs to the Section Medical Biotechnology)

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18 pages, 1301 KiB

Open AccessArticle

Prediction of Lupus Classification Criteria via Generative AI Medical Record Profiling

by Sandeep Nair, Gerald H. Lushington, Mohan Purushothaman, Bernard Rubin, Eldon Jupe and Santosh Gattam

BioTech 2025, 14(1), 15; https://doi.org/10.3390/biotech14010015 - 6 Mar 2025

Viewed by 607

Abstract

Systemic lupus erythematosus (SLE) is a complex autoimmune disease that poses serious long-term patient burdens. (1) Background: SLE patient classification and care are often complicated by case heterogeneity (diverse variations in symptoms and severity). Large language models (LLMs) and generative artificial intelligence (genAI) [...] Read more.

Systemic lupus erythematosus (SLE) is a complex autoimmune disease that poses serious long-term patient burdens. (1) Background: SLE patient classification and care are often complicated by case heterogeneity (diverse variations in symptoms and severity). Large language models (LLMs) and generative artificial intelligence (genAI) may mitigate this challenge by profiling medical records to assess key medical criteria. (2) Methods: To demonstrate genAI-based profiling, ACR (American College of Rheumatology) 1997 SLE classification criteria were used to define medically relevant LLM prompts. Records from 78 previously studied patients (45 classified as having SLE; 33 indeterminate or negative) were computationally profiled, via five genAI replicate runs. (3) Results: GenAI determinations of the “Discoid Rash” and “Pleuritis or Pericarditis” classification criteria yielded perfect concurrence with clinical classification, while some factors such as “Immunologic Disorder” (56% accuracy) were statistically unreliable. Compared to clinical classification, our genAI approach achieved a 72% predictive success rate. (4) Conclusions: GenAI classifications may prove sufficiently predictive to aid medical professionals in evaluating SLE patients and structuring care strategies. For individual criteria, accuracy seems to correlate inversely with complexities in clinical determination, implying that improvements in AI patient profiling tools may emerge from continued advances in clinical classification efficacy. Full article

(This article belongs to the Topic Computational Intelligence and Bioinformatics (CIB))

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28 pages, 1169 KiB

Open AccessReview

Phytohormonal Regulation of Abiotic Stress Tolerance, Leaf Senescence and Yield Response in Field Crops: A Comprehensive Review

by Anna Panozzo, Pranay Kumar Bolla, Giuseppe Barion, Alessandro Botton and Teofilo Vamerali

BioTech 2025, 14(1), 14; https://doi.org/10.3390/biotech14010014 - 27 Feb 2025

Cited by 1 | Viewed by 733

Abstract

Field crops are expected to be increasingly threatened by climate change, which will negatively impact plant development, growth and yield. Phytohormones play a crucial role in regulating specific signalling pathways to induce rapid adaptive responses to environmental stresses. Exogenous phytohormone application alters hormonal [...] Read more.

Field crops are expected to be increasingly threatened by climate change, which will negatively impact plant development, growth and yield. Phytohormones play a crucial role in regulating specific signalling pathways to induce rapid adaptive responses to environmental stresses. Exogenous phytohormone application alters hormonal balance, thereby enhancing plant adaptation to adverse conditions. While several studies have advanced our understanding of the use of phytohormones in field crops, yield responses and species-specific application strategies remain inconsistent and rarely assessed under field conditions. The application of cytokinins (CKs), abscisic acid (ABA), and gibberellic acid (GA) has been shown to maintain prolonged photosynthetic activity, stabilize plasma membrane, and reduce lipid peroxidation and ion accumulation under salinity stress in wheat. Additionally, inhibitors of ethylene synthesis and receptors can mitigate stress symptoms under drought and heat stress, which typically accelerates senescence and shortens the grain-filling period in cereal crops. In this way, exogenous application of CKs, GA, and ethylene inhibitors can delay senescence by sustaining leaf photosynthetic activity and postponing nutrient remobilization. However, these benefits may not consistently translate into improvements in grain yield and quality. This review explores the molecular mechanisms of phytohormones in abiotic stress tolerance, delineates their specific functions and evaluates experimental findings from field applications. It also summarizes the potential of phytohormone applications in field crops, emphasizing the need for species-specific investigations on application timing and dosages under open-field conditions to optimize their agronomic potential. Full article

(This article belongs to the Section Industry, Agriculture and Food Biotechnology)

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30 pages, 4871 KiB

Open AccessArticle

Structure-Based Modeling of the Gut Bacteria–Host Interactome Through Statistical Analysis of Domain–Domain Associations Using Machine Learning

by Despoina P. Kiouri, Georgios C. Batsis, Thomas Mavromoustakos, Alessandro Giuliani and Christos T. Chasapis

BioTech 2025, 14(1), 13; https://doi.org/10.3390/biotech14010013 - 25 Feb 2025

Viewed by 484

Abstract

The gut microbiome, a complex ecosystem of microorganisms, plays a pivotal role in human health and disease. The gut microbiome’s influence extends beyond the digestive system to various organs, and its imbalance is linked to a wide range of diseases, including cancer and [...] Read more.

The gut microbiome, a complex ecosystem of microorganisms, plays a pivotal role in human health and disease. The gut microbiome’s influence extends beyond the digestive system to various organs, and its imbalance is linked to a wide range of diseases, including cancer and neurodevelopmental, inflammatory, metabolic, cardiovascular, autoimmune, and psychiatric diseases. Despite its significance, the interactions between gut bacteria and human proteins remain understudied, with less than 20,000 experimentally validated protein interactions between the host and any bacteria species. This study addresses this knowledge gap by predicting a protein–protein interaction network between gut bacterial and human proteins. Using statistical associations between Pfam domains, a comprehensive dataset of over one million experimentally validated pan-bacterial–human protein interactions, as well as inter- and intra-species protein interactions from various organisms, were used for the development of a machine learning-based prediction method to uncover key regulatory molecules in this dynamic system. This study’s findings contribute to the understanding of the intricate gut microbiome–host relationship and pave the way for future experimental validation and therapeutic strategies targeting the gut microbiome interplay. Full article

(This article belongs to the Section Computational Biology)

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15 pages, 3580 KiB

Open AccessArticle

Enhanced Bioactive Compounds and Antioxidant Activity in Germinated Seeds of the New Peanut Variety

by Hwan-Hee Yu, Jong-Suk Park and Sanghyun Lee

BioTech 2025, 14(1), 12; https://doi.org/10.3390/biotech14010012 - 25 Feb 2025

Cited by 1 | Viewed by 444

Abstract

The sprout market in Korea is expanding as consumers seek healthier food options and farmers strive to increase added value and competitiveness. This study examined the changes in the phytochemical composition of Sinpalkwang (SPK), a peanut variety developed in Korea, during germination. Four [...] Read more.

The sprout market in Korea is expanding as consumers seek healthier food options and farmers strive to increase added value and competitiveness. This study examined the changes in the phytochemical composition of Sinpalkwang (SPK), a peanut variety developed in Korea, during germination. Four samples (SPK1, SPK2, SPK3, and SPK4) were collected at different growth stages and analyzed for total polyphenol content (TPC), total flavonoid content (TFC), and antioxidant activities using ABTS⁺ and DPPH assays. The levels of trans-resveratrol and soyasaponin Bb were quantified using high-performance liquid chromatography (HPLC) with a photo-diode array (PDA). Among the samples, SPK2 exhibited the highest TFC (1.61 mg QE/g ext.) and trans-resveratrol content (0.054 mg/g ext.), while SPK4 showed the highest TPC (29.38 mg TAE/g ext.) and soyasaponin Bb content (6.543 mg/g ext.). In terms of radical scavenging activities, SPK2 and SPK3 performed best in the ABTS⁺ and DPPH assays, respectively. Germinated samples demonstrated strong results across all analyses, highlighting the benefits of germination in enhancing phytochemical properties. This study provides foundational information on the phytochemical composition of SPK and the effects of germination. Future research will focus on optimizing germination conditions to further enhance the functionality and value of this Korean-bred variety as a source of high-value bioactive ingredients. Full article

(This article belongs to the Special Issue Natural Antioxidants: Determination in Food and Nutraceuticals and Implications on Human Health)

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16 pages, 1345 KiB

Open AccessReview

STXBP1 Syndrome: Biotechnological Advances, Challenges, and Perspectives in Gene Therapy, Experimental Models, and Translational Research

by Silvestre Ruano-Rodríguez, Mar Navarro-Alonso, Benito Domínguez-Velasco, Manuel Álvarez-Dolado and Francisco J. Esteban

BioTech 2025, 14(1), 11; https://doi.org/10.3390/biotech14010011 - 20 Feb 2025

Viewed by 1182

Abstract

STXBP1 syndrome is a severe early-onset epileptic encephalopathy characterized by developmental delay and intellectual disability. This review addresses key challenges in STXBP1 syndrome research, focusing on advanced therapeutic approaches and experimental models. We explore gene therapy strategies, including CRISPR-Cas9, adeno-associated viral (AAV) vectors, [...] Read more.

STXBP1 syndrome is a severe early-onset epileptic encephalopathy characterized by developmental delay and intellectual disability. This review addresses key challenges in STXBP1 syndrome research, focusing on advanced therapeutic approaches and experimental models. We explore gene therapy strategies, including CRISPR-Cas9, adeno-associated viral (AAV) vectors, and RNA therapies such as antisense oligonucleotides (ASOs), aimed at correcting STXBP1 genetic dysfunctions. This review presents in vivo and in vitro models, highlighting their contributions to understanding disease mechanisms. Additionally, we provide a proposal for a detailed bioinformatic analysis of a Spanish cohort of 41 individuals with STXBP1-related disorders, offering insights into specific mutations and their biological implications. Clinical and translational perspectives are discussed, emphasizing the potential of personalized medicine approaches. Future research directions and key challenges are outlined, including the identification of STXBP1 interactors, unexplored molecular pathways, and the need for clinically useful biomarkers. This comprehensive review underscores the complexity of STXBP1-related infantile epileptic encephalopathy and opens new avenues for advancing the understanding and treatment of this heterogeneous disease. Full article

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13 pages, 2651 KiB

Open AccessArticle

A Live-Cell Imaging-Based Fluorescent SARS-CoV-2 Neutralization Assay by Antibody-Mediated Blockage of Receptor Binding Domain-ACE2 Interaction

by Jorge L. Arias-Arias, Laura Monturiol-Gross and Eugenia Corrales-Aguilar

BioTech 2025, 14(1), 10; https://doi.org/10.3390/biotech14010010 - 14 Feb 2025

Viewed by 701

Abstract

Neutralization assays have become an important tool since the beginning of the COVID-19 pandemic for testing vaccine responses and therapeutic antibodies as well as for monitoring humoral immunity to SARS-CoV-2 in epidemiological studies. The spike glycoprotein (S) present on the viral surface contains [...] Read more.

Neutralization assays have become an important tool since the beginning of the COVID-19 pandemic for testing vaccine responses and therapeutic antibodies as well as for monitoring humoral immunity to SARS-CoV-2 in epidemiological studies. The spike glycoprotein (S) present on the viral surface contains a receptor binding domain (RBD) that recognizes the angiotensin-converting enzyme 2 receptor (ACE2) in host cells, allowing virus entry. The gold standard for determining SARS-CoV-2 neutralizing antibodies is the plaque reduction neutralization test (PRNT), which relies on live-virus replication performed exclusively in biosafety level 3 (BSL-3) laboratories. Here, we report the development of a surrogate live-cell imaging-based fluorescent SARS-CoV-2 neutralization assay, applicable to BSL-1 or BSL-2 laboratories, by antibody-mediated blockage of the interaction between recombinant RBD with overexpressed ACE2 receptor in a genetically modified HEK 293T stable cell line. Our approach was able to detect neutralizing antibodies both in COVID-19-positive human serum samples and polyclonal equine formulations against SARS-CoV-2. This new cell-based surrogate neutralization assay represents a virus-free fluorescence imaging alternative to the reported approaches, which can be used to detect antibody-neutralizing capabilities toward SARS-CoV-2. This assay could also be extrapolated in the future to other established and emergent viral agents. Full article

(This article belongs to the Special Issue Advances in Bioimaging Technology)

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13 pages, 1850 KiB

Open AccessArticle

Bioinformatics Tools for NGS-Based Identification of Single Nucleotide Variants and Large-Scale Rearrangements in Mitochondrial DNA

by Marco Barresi, Giulia Dal Santo, Rossella Izzo, Andrea Zauli, Eleonora Lamantea, Leonardo Caporali, Daniele Ghezzi and Andrea Legati

BioTech 2025, 14(1), 9; https://doi.org/10.3390/biotech14010009 - 12 Feb 2025

Viewed by 885

Abstract

The unique features of mitochondrial DNA (mtDNA), including its circular and multicopy nature, the possible coexistence of wild-type and mutant molecules (i.e., heteroplasmy) and the presence of nuclear mitochondrial DNA segments (NUMTs), make the diagnosis of mtDNA diseases particularly challenging. The extensive deployment [...] Read more.

The unique features of mitochondrial DNA (mtDNA), including its circular and multicopy nature, the possible coexistence of wild-type and mutant molecules (i.e., heteroplasmy) and the presence of nuclear mitochondrial DNA segments (NUMTs), make the diagnosis of mtDNA diseases particularly challenging. The extensive deployment of next-generation sequencing (NGS) technologies has significantly advanced the diagnosis of mtDNA-related diseases. However, the vast amounts and diverse types of sequencing data complicate the interpretation of these variants. From sequence alignment to variant calling, NGS-based mtDNA sequencing requires specialized bioinformatics tools, adapted for the mitochondrial genome. This study presents the use of new bioinformatics approaches, optimized for short- and long-read sequencing data, to enhance the accuracy of mtDNA analysis in diagnostics. Two recent and emerging free bioinformatics tools, Mitopore and MitoSAlt, were evaluated on patients previously diagnosed with single nucleotide variants or large-scale deletions. Analyses were performed in Linux-based environments and web servers implemented in Python, Perl, Java, and R. The results indicated that each tool demonstrated high sensitivity and specific accuracy in identifying and quantifying various types of pathogenic variants. The study suggests that the integrated and parallel use of these tools offers a significant advantage over traditional methods in interpreting mtDNA genetic variants, reducing the computational demands, and provides an accurate diagnostic solution. Full article

(This article belongs to the Section Computational Biology)

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18 pages, 937 KiB

Open AccessReview

Recent Advances in Scaling up Bioelectrochemical Systems: A Review

by Diego A. Corona-Martínez, Silvia Y. Martínez-Amador, José A. Rodríguez-De la Garza, Elan I. Laredo-Alcalá and Pedro Pérez-Rodríguez

BioTech 2025, 14(1), 8; https://doi.org/10.3390/biotech14010008 - 31 Jan 2025

Viewed by 1065

Abstract

Bioelectrochemical systems (BESs) are devices capable of converting chemical energy into electrical energy using microorganisms as catalysts. These systems have been extensively studied at the laboratory level, but, due to multiple difficulties, their large-scale implementation has been explored only sparingly. This study presents [...] Read more.

Bioelectrochemical systems (BESs) are devices capable of converting chemical energy into electrical energy using microorganisms as catalysts. These systems have been extensively studied at the laboratory level, but, due to multiple difficulties, their large-scale implementation has been explored only sparingly. This study presents the most recent technological advances for scaling up BESs. In the same way, the main technical and economic challenges that hinder the correct implementation of these systems at a large scale are mentioned. The study concludes with a review of successful case studies in scaling up BESs and discusses future directions and emerging trends. Full article

(This article belongs to the Section Industry, Agriculture and Food Biotechnology)

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34 pages, 1515 KiB

Open AccessReview

The Use of Biologics for Targeting GPCRs in Metastatic Cancers

by Cian McBrien and David J. O’Connell

BioTech 2025, 14(1), 7; https://doi.org/10.3390/biotech14010007 - 30 Jan 2025

Viewed by 2618

Abstract

A comprehensive review of studies describing the role of G-protein coupled receptor (GPCR) behaviour contributing to metastasis in cancer, and the developments of biotherapeutic drugs towards targeting them, provides a valuable resource toward improving our understanding of the opportunities to effectively target this [...] Read more.

A comprehensive review of studies describing the role of G-protein coupled receptor (GPCR) behaviour contributing to metastasis in cancer, and the developments of biotherapeutic drugs towards targeting them, provides a valuable resource toward improving our understanding of the opportunities to effectively target this malignant tumour cell adaptation. Focusing on the five most common metastatic cancers of lung, breast, colorectal, melanoma, and prostate cancer, we highlight well-studied and characterised GPCRs and some less studied receptors that are also implicated in the development of metastatic cancers. Of the approximately 390 GPCRs relevant to therapeutic targeting, as many as 125 of these have been identified to play a role in promoting metastatic disease in these cancer types. GPCR signalling through the well-characterised pathways of chemokine receptors, to emerging data on signalling by orphan receptors, is integral to many aspects of the metastatic phenotype. Despite having detailed information on many receptors and their ligands, there are only thirteen approved therapeutics specifically for metastatic cancer, of which three are small molecules with the remainder including synthetic and non-synthetic peptides or monoclonal antibodies. This review will cover the existing and potential use of monoclonal antibodies, proteins and peptides, and nanobodies in targeting GPCRs for metastatic cancer therapy. Full article

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30 pages, 884 KiB

Open AccessReview

Aromatic Amino Acids: Exploring Microalgae as a Potential Biofactory

by Archana Niraula, Amir Danesh, Natacha Merindol, Fatma Meddeb-Mouelhi and Isabel Desgagné-Penix

BioTech 2025, 14(1), 6; https://doi.org/10.3390/biotech14010006 - 29 Jan 2025

Viewed by 1592

Abstract

In recent times, microalgae have emerged as powerful hosts for biotechnological applications, ranging from the production of lipids and specialized metabolites (SMs) of pharmaceutical interest to biofuels, nutraceutical supplements, and more. SM synthesis through bioengineered pathways relies on the availability of aromatic amino [...] Read more.

In recent times, microalgae have emerged as powerful hosts for biotechnological applications, ranging from the production of lipids and specialized metabolites (SMs) of pharmaceutical interest to biofuels, nutraceutical supplements, and more. SM synthesis through bioengineered pathways relies on the availability of aromatic amino acids (AAAs) as an essential precursor. AAAs, phenylalanine, tyrosine, and tryptophan are also the building blocks of proteins, maintaining the structural and functional integrity of cells. Hence, they are crucial intermediates linking the primary and specialized metabolism. The biosynthesis pathway of AAAs in microbes and plants has been studied for decades, but not much is known about microalgae. The allosteric control present in this pathway has been targeted for metabolic engineering in microbes. This review focuses on the biosynthesis of AAAs in eukaryotic microalgae and engineering techniques for enhanced production. All the putative genes involved in AAA pathways in the model microalgae Chlamydomonas reinhardtii and Phaeodactylum tricornutum are listed in this review. Full article

(This article belongs to the Section Industry, Agriculture and Food Biotechnology)

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19 pages, 3649 KiB

Open AccessArticle

Evaluating TcAs for Use in Biotechnology Applications

by Cole L. Martin, John H. Hill, Brian D. Wright, Solana R. Fernandez, Aubrey L. Miller, Karina J. Yoon, Suzanne E. Lapi and Stephen G. Aller

BioTech 2025, 14(1), 5; https://doi.org/10.3390/biotech14010005 - 25 Jan 2025

Viewed by 1079

Abstract

ABC toxin complexes (Tcs) are tripartite complexes that come together to form nano-syringe-like translocation systems. ABC Tcs are often compared with Bacillus thuringiensis (Bt) toxins, and as such, they have been highly studied as a potential novel pesticide to combat growing insect resistance. [...] Read more.

ABC toxin complexes (Tcs) are tripartite complexes that come together to form nano-syringe-like translocation systems. ABC Tcs are often compared with Bacillus thuringiensis (Bt) toxins, and as such, they have been highly studied as a potential novel pesticide to combat growing insect resistance. Moreover, it is possible to substitute the cytotoxic hypervariable region with alternative peptides, which promise potential use as a novel peptide delivery system. These toxins possess the unique ability to form active chimeric holotoxins across species and display the capability to translocate a variety of payloads across membrane bilayers. Additionally, mutagenesis on the linker region and the receptor binding domains (RBDs) show that mutations do not inherently cause a loss of functionality for translocation. For these reasons, Tcs have emerged as an ideal candidate for targeted protein engineering. However, elucidation of the specific function of each RBD in relation to target receptor recognition currently limits the use of a rational design approach with any ABC Tc. Additionally, there is a distinct lack of targeting and biodistribution data for many Tcs among mammals and mammalian cell lines. Here, we outline two separate strategies for modifying the targeting capabilities of the A subunit (TcA) from Xenorhabdus nematophilus, Xn-XptA2. We identify novel structural differences that make Xn-XptA2 different than other characterized TcAs and display the modular capabilities of substituting RBDs from alternative TcAs into the Xn-XptA2 scaffold. Finally, we show the first, to our knowledge, biodistribution data of any TcA in mice. Full article

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20 pages, 2534 KiB

Open AccessArticle

Discovery of Innate Immune Response mRNAs That Are Impacted by Structure-Specific Oral Baker’s Yeast Beta Glucan Consumption

by Brian K. McFarlin, John H. Curtis, Jakob L. Vingren, David W. Hill and Elizabeth A. Bridgeman

BioTech 2025, 14(1), 4; https://doi.org/10.3390/biotech14010004 - 13 Jan 2025

Viewed by 866

Abstract

The study of nutritional compounds with the potential to train the innate immune response has implications for human health. The objective of the current study was to discover by what means 6 weeks of oral baker’s yeast beta glucan (BYBG) supplementation altered the [...] Read more.

The study of nutritional compounds with the potential to train the innate immune response has implications for human health. The objective of the current study was to discover by what means 6 weeks of oral baker’s yeast beta glucan (BYBG) supplementation altered the mRNA expression of genes that reflect innate immune training in the absence of a physical stressor. Nineteen adults were randomly assigned to either a Wellmune^® BYBG or Placebo for 6 weeks. BYBG uniquely altered the expression of 40 mRNAs associated with Dectin-1 and trained innate immunity, the innate immune response, the pathogen-associated (PAMP) and damage-associated molecular pattern (DAMP), and the inflammatory response. The observed changes were classified as immune training rather than immune priming due to the progressive increase in the expression of myeloid immune-associated mRNA. Combined with the findings of previous research, the findings of the present study support the claim that oral BYBG supplementation may be associated with trained innate immunity during resting homeostasis. Further, the key findings associated with BYBG may reflect improved responsiveness to future infection (exogenous) and/or sterile-inflammatory (endogenous) challenge. Full article

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29 pages, 2633 KiB

Open AccessReview

Current Approaches for Genetic Manipulation of Streptomyces spp.—Key Bacteria for Biotechnology and Environment

by Sergii Krysenko

BioTech 2025, 14(1), 3; https://doi.org/10.3390/biotech14010003 - 2 Jan 2025

Viewed by 1438

Abstract

Organisms from the genus Streptomyces feature actinobacteria with complex developmental cycles and a great ability to produce a variety of natural products. These soil bacteria produce more than 2/3 of antibiotics used in medicine, and a large variety of bioactive compounds for industrial, [...] Read more.

Organisms from the genus Streptomyces feature actinobacteria with complex developmental cycles and a great ability to produce a variety of natural products. These soil bacteria produce more than 2/3 of antibiotics used in medicine, and a large variety of bioactive compounds for industrial, medical and agricultural use. Although Streptomyces spp. have been studied for decades, the engineering of these bacteria remains challenging, and the available genetic tools are rather limited. Furthermore, most biosynthetic gene clusters in these bacteria are silent and require strategies to activate them and exploit their production potential. In order to explore, understand and manipulate the capabilities of Streptomyces spp. as a key bacterial for biotechnology, synthetic biology strategies emerged as a valuable component of Streptomyces research. Recent advancements in strategies for genetic manipulation of Streptomyces involving proposals of a large variety of synthetic components for the genetic toolbox, as well as new approaches for genome mining, assembly of genetic constructs and their delivery into the cell, allowed facilitation of the turnaround time of strain engineering and efficient production of new natural products at an industrial scale, but still have strain- and design-dependent limitations. A new perspective offered recently by technical advances in DNA sequencing, analysis and editing proposed strategies to overcome strain- and construct-specific difficulties in the engineering of Streptomyces. In this review, challenges and recent developments of approaches for Streptomyces engineering are discussed, an overview of novel synthetic biology strategies is provided and examples of successful application of new technologies in molecular genetic engineering of Streptomyces are highlighted. Full article

(This article belongs to the Section Industry, Agriculture and Food Biotechnology)

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12 pages, 1400 KiB

Open AccessArticle

Impact of GAUT1 Gene Knockout on Cell Aggregation in Arabidopsis thaliana Suspension Culture

by Tatyana A. Frankevich, Natalya V. Permyakova, Yury V. Sidorchuk and Elena V. Deineko

BioTech 2025, 14(1), 2; https://doi.org/10.3390/biotech14010002 - 2 Jan 2025

Cited by 1 | Viewed by 979

Abstract

The development of efficient producers of recombinant pharmaceuticals based on plant cell suspension cultures is a pressing challenge in modern applied science. A primary limitation of plant cell cultures is their relatively low yield of the target protein. One strategy to enhance culture [...] Read more.

The development of efficient producers of recombinant pharmaceuticals based on plant cell suspension cultures is a pressing challenge in modern applied science. A primary limitation of plant cell cultures is their relatively low yield of the target protein. One strategy to enhance culture productivity involves reducing cell aggregation. In order to minimize cell-to-cell adhesion in culture, we used Cas9 endonuclease to knock out the GAUT1 gene, which is a key gene of pectin biosynthesis in the genome of Arabidopsis thaliana. The resulting knockouts exhibited altered phenotypes and were unable to form viable plants. The suspension cell culture induced from seedlings bearing a homozygous deletion in the GAUT1 gene displayed darker coloration and an increased number of large aggregates compared to the control. The biomass accumulation rate showed no difference from the control, while the level of recombinant GFP protein accumulation was significantly reduced. Thus, our findings indicate that disruptions in pectin synthesis and the formation of larger aggregates in the suspension cell culture adversely affect the accumulation of the target recombinant protein. Alternative targets should be sought to reduce cell aggregation levels in plant cell cultures through genome editing. Full article

(This article belongs to the Section Industry, Agriculture and Food Biotechnology)

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Graphical abstract

24 pages, 10317 KiB

Open AccessArticle

Peptide Inhibitor Assay for Allocating Functionally Important Accessible Sites Throughout a Protein Chain: Restriction Endonuclease EcoRI as a Model Protein System

by Joji M. Otaki

BioTech 2025, 14(1), 1; https://doi.org/10.3390/biotech14010001 - 30 Dec 2024

Viewed by 725

Abstract

Functionally important amino acid sequences in proteins are often located at multiple sites. Three-dimensional structural analysis and site-directed mutagenesis may be performed to allocate functional sites for understanding structure‒function relationships and for developing novel inhibitory drugs. However, such methods are too demanding to [...] Read more.

Functionally important amino acid sequences in proteins are often located at multiple sites. Three-dimensional structural analysis and site-directed mutagenesis may be performed to allocate functional sites for understanding structure‒function relationships and for developing novel inhibitory drugs. However, such methods are too demanding to comprehensively cover potential functional sites throughout a protein chain. Here, a peptide inhibitor assay (PIA) was devised to allocate functionally important accessible sites in proteins. This simple method presumes that protein‒ligand interactions, intramolecular interactions, and dimerization interactions can be partially inhibited by high concentrations of competitive “endogenous” peptides of the protein of interest. Focusing on the restriction endonuclease EcoRI as a model protein system, many endogenous peptides (6mer-14mer) were synthesized, covering the entire EcoRI protein chain. Some of them were highly inhibitory, but interestingly, the nine most effective peptides were located outside the active sites, with the exception of one. Relatively long peptides with aromatic residues (F, H, W, and Y) corresponding to secondary structures were generally effective. Because synthetic peptides are flexible enough to change length and amino acid residues, this method may be useful for quickly and comprehensively understanding structure‒function relationships and developing novel drugs or epitopes for neutralizing antibodies. Full article

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BioTech, Volume 14, Issue 1 (March 2025) – 23 articles

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