BioTech

41 pages, 731 KB

Open AccessReview

Gene Flow and Hybridization Potential Between GM/NGT Crops and Conventional Varieties or Wild Relatives: A Scoping Literature Review with Emphasis on Oilseed Rape (Brassica napus L.) and Potato (Solanum tuberosum L.)

by Lelde Grantina-Ievina and Nils Rostoks

BioTech 2026, 15(2), 30; https://doi.org/10.3390/biotech15020030 - 8 Apr 2026

Abstract

Genetically modified (GM) plants have been commercially grown for 30 years, and their acceptance depends on a thorough risk assessment. Environmental Risk Assessment (ERA) evaluates potential impacts of releasing GM plants into the environment, whether through cultivation or import for food, feed, and [...] Read more.

Genetically modified (GM) plants have been commercially grown for 30 years, and their acceptance depends on a thorough risk assessment. Environmental Risk Assessment (ERA) evaluates potential impacts of releasing GM plants into the environment, whether through cultivation or import for food, feed, and processing. A key component is assessing potential gene flow to crop wild relatives or non-GM crops. For gene flow to significantly affect the environment, transferred genes must provide a selective advantage. Since most GM plants are engineered for herbicide tolerance, insect resistance, or stacked traits, evaluating such advantages is relatively straightforward. New genomic techniques (NGTs) can generate plants with a wider range of traits, including tolerance to biotic and abiotic stress. Although still considered GM in the EU, their genomic changes can complicate detection, identification, and ERA, especially when such traits may offer advantages under stress conditions. This scoping review focuses on gene flow in two crops: oilseed rape (canola) (Brassica napus L.) and potato (Solanum tuberosum L.). In canola, transgene movement can increase weediness, fitness, herbicide resistance, or genetic diversity in feral or related populations. Gene flow in potato is less studied, with concerns centered on contamination risks in the Andean diversity center. Limited data exist for NGT plants, though many are expected to resemble conventionally bred varieties, suggesting comparable environmental impacts. Full article

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

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18 pages, 3332 KB

Open AccessArticle

DFT Calculations on Electronic, Thermochemical and Vibrational Properties of Se₆ Selenium Clusters as 5-Fluorouracil Drug Delivery System

by Levi Isai Solano-González, Raúl Mendoza-Báez, Ricardo Agustín-Serrano, José Isrrael Rodríguez-Mora and Marco A. Morales

BioTech 2026, 15(2), 29; https://doi.org/10.3390/biotech15020029 - 31 Mar 2026

Abstract

In this work, the electronic, thermochemical, and vibrational characterization of the drug delivery system formed by clusters of selenium (Se₆ allotrope) and 5-fluorouracil (5-FU) are studied, based on density functional theory (DFT) calculations. Computational calculations were performed using the B3LYP functional and [...] Read more.

In this work, the electronic, thermochemical, and vibrational characterization of the drug delivery system formed by clusters of selenium (Se₆ allotrope) and 5-fluorouracil (5-FU) are studied, based on density functional theory (DFT) calculations. Computational calculations were performed using the B3LYP functional and the 6-31G(d,p) base set, considering an aqueous medium through the CPCM solvation model. We propose evaluating two different interaction modes based on experimental observations: Se–H(N) (through the amino groups of 5-FU) and Se–O(C) (through the carbonyl oxygen of 5-FU). All complexes proved to be energetically stable, exhibiting chemisorption as their adsorption process. Analysis of adsorption energy and thermodynamic parameters indicates that both interaction pathways are equally viable, which agrees with previous experimental findings. The theoretical FT-IR spectra of these complexes also coincide with the experimental results. Furthermore, global molecular descriptors show that the stability of the selenium carrier is not affected by post-functionalization, which is desirable for more controlled drug delivery systems. Full article

(This article belongs to the Section Computational Biology)

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24 pages, 3457 KB

Open AccessArticle

Hypoxia and DNA-Repair Radiosensitivity Signatures Are Associated with Radiotherapy-Modified Survival in TCGA Breast Cancer, with External Prognostic Validation of the Hypoxia Score in METABRIC

by Jimmy Carter Osei, Mei-Han Chen and Tim A. D. Smith

BioTech 2026, 15(2), 28; https://doi.org/10.3390/biotech15020028 - 31 Mar 2026

Abstract

Radiotherapy (RT) is one of the main treatments for breast cancer, but response varies between patients. Tumour hypoxia and intrinsic radiosensitivity are major determinants of response to RT. Using TCGA-BRCA, a 563-gene hypoxia meta-signature was built by combining curated hypoxia gene sets from [...] Read more.

Radiotherapy (RT) is one of the main treatments for breast cancer, but response varies between patients. Tumour hypoxia and intrinsic radiosensitivity are major determinants of response to RT. Using TCGA-BRCA, a 563-gene hypoxia meta-signature was built by combining curated hypoxia gene sets from MSigDB with published hypoxia metagenes (Buffa, Winter, Elvidge, Fardin, and related sets). After Cox screening and penalised regression, a simple three-gene hypoxia score (CP, GPC3, STC1) was derived. In parallel, based on DSB-repair factors highlighted by Mladenov et al. as key regulators of intrinsic radiosensitivity, a four-gene radiosensitivity (RS) signature (ATR, RPA2, BLM, MRE11A) was trained using only RT-treated patients. In TCGA, both signatures were prognostic and showed significant interaction with RT status in Cox models. The hypoxia score was strongly associated with worse outcomes in RT-untreated patients, but this effect was much weaker in RT-treated patients (Hypoxia × RT HR = 0.009, p = 0.044). The RS score showed a similarly strong interaction with RT (RS × RT HR = 0.011, p = 0.003). When we combined both signatures into one interaction model, it gave the best performance (C-index = 0.785), and both interaction terms stayed independently significant. The hypoxia score was then validated externally in METABRIC (N = 1979; 1143 events), where it remained associated with overall survival, although more weakly than in TCGA (HR = 1.34, 95% CI: 1.10–1.63; p = 0.0042). Overall, these results suggest that hypoxia and DSB-repair capacity capture two complementary sides of radiosensitivity and RT-modified survival patterns, and they support further prospective testing and validation in independent datasets with strong RT annotation. Full article

(This article belongs to the Special Issue The Emerging Role of Bioinformatics in Biotechnology)

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17 pages, 1997 KB

Open AccessArticle

Bioremediation of Lubricant Oil by Environmentally Adapted Pseudomonas aeruginosa, Pseudomonas putida, and Proteus vulgaris in Houston, Texas

by Sadith Mosquera and Jason A. Rosenzweig

BioTech 2026, 15(2), 27; https://doi.org/10.3390/biotech15020027 - 26 Mar 2026

Abstract

Lubricating oil (LO) is manufactured in various formulations for different applications. The inappropriate disposal of petroleum hydrocarbons can increase soil contamination, promoting deleterious environmental and human health impacts. More specifically, following prolonged exposure, LO contaminants are known to have carcinogenic and neurotoxic effects [...] Read more.

Lubricating oil (LO) is manufactured in various formulations for different applications. The inappropriate disposal of petroleum hydrocarbons can increase soil contamination, promoting deleterious environmental and human health impacts. More specifically, following prolonged exposure, LO contaminants are known to have carcinogenic and neurotoxic effects in humans. Bioremediation provides an effective and attractive strategy to expedite the clean-up processes of LO contaminants. We isolated and identified environmentally adapted strains of Pseudomonas aeruginosa, Pseudomonas putida, and Proteus vulgaris from Houston watershed bayou soils. Interestingly, all three exhibited increased resistance, vis-a-vis surrogate strains, to various antibiotic challenges (of chloramphenicol, tetracycline, kanamycin, penicillin, streptomycin, etc.) and increased biofilm formation ranging from 1.6 to 6.7-fold. In fact, all three environmental strains were significantly better at producing enhanced biofilm formation in the presence of spent LO rather than clean LO as well as outproducing biofilm made by the surrogate strains. Finally, the environmental isolates P. aeruginosa, P. putida, and P. vulgaris demonstrated an enhanced ability to sequester clean (2-, 2.5- and 1.14-fold) and spent (1.4-, 1.5, and 1.2-fold) LO when compared to their commercially acquired surrogate reference strains. Our three environmentally isolated organisms from Houston watershed soils appeared to be environmentally adapted to tolerate LO exposures. In the presence of LOs, all three environmentally isolated strains exhibited enhanced growth, enhanced biofilm production, and improved bioaccumulation of LOs relative to commercial reference strains. Taken together, environmentally adapted organisms can promote the bioremediation of contaminants threatening our environment and, potentially, human health. Full article

(This article belongs to the Section Environmental Biotechnology)

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21 pages, 896 KB

Open AccessArticle

Biotechnological Potential of Yucca decipiens Trel Based on Proximate Composition, Multi-Elemental Analysis, and Nursery Growth Performance

by Selena del Rocío Martínez-Betancourt, Jorge Cadena-Iñiguez, Laura Araceli López-Martínez, Janet María León Morales, Ramón Marcos Soto-Hernández, Gerardo Loera-Alvarado, Víctor Manuel Ruiz-Vera and Concepción López-Padilla

BioTech 2026, 15(2), 26; https://doi.org/10.3390/biotech15020026 - 25 Mar 2026

Abstract

Yucca decipiens is a native species from arid and semi-arid regions with emerging nutritional and biotechnological potential. This study evaluated its proximate composition, elemental profile determined by inductively coupled plasma mass spectrometry (ICP-MS), and growth performance under nursery conditions. Proximate analysis revealed a [...] Read more.

Yucca decipiens is a native species from arid and semi-arid regions with emerging nutritional and biotechnological potential. This study evaluated its proximate composition, elemental profile determined by inductively coupled plasma mass spectrometry (ICP-MS), and growth performance under nursery conditions. Proximate analysis revealed a high dietary fiber content in leaves (58.93%) and higher carbohydrate levels in stems (28.83%). Free amino acid content was significantly higher in stems (2.75 g histidine equivalents kg⁻¹) than in leaves (1.76 g kg⁻¹). Multi-elemental profiling (63 elements) showed organ-specific accumulation patterns, with essential macro- and micronutrients predominantly concentrated in leaves, including potassium (28,334 ppm) and calcium (15,345 ppm), while iron was the most abundant trace element in stems (1253 ppm). Principal component analysis (PCA) revealed clear organ-specific mineral partitioning between leaves and stems, indicating differentiated physiological roles and potential selective biomass utilization. Growth assessment conducted over a two-year period demonstrated steady biomass accumulation and good adaptive performance under nursery conditions. Overall, the results highlight the emerging nutritional and agroindustrial relevance of Yucca decipiens for applications in semi-arid environments. Full article

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

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26 pages, 3881 KB

Open AccessArticle

Characterization and Biological Activity of Rutin Extracted from Filipendula ulmaria (L.) Maxim

by Anna Vesnina, Violeta Le, Svetlana Ivanova, Anna Frolova, Irina Milentyeva, Victor Atuchin and Alexander Prosekov

BioTech 2026, 15(1), 25; https://doi.org/10.3390/biotech15010025 - 23 Mar 2026

Abstract

In this work, Filipendula ulmaria (L.) Maxim, a perennial herbaceous plant from the Rosaceae family, was considered a novel source of obtaining rutin for pharmaceutical purposes. Rutin was extracted from the plant parts collected in the flowering summer period and dried at 40 [...] Read more.

In this work, Filipendula ulmaria (L.) Maxim, a perennial herbaceous plant from the Rosaceae family, was considered a novel source of obtaining rutin for pharmaceutical purposes. Rutin was extracted from the plant parts collected in the flowering summer period and dried at 40 ± 3 °C. The process was carried out using the ethanol extraction and fractionation of extracted compounds, and it yields the 95 wt% purity crystalline product. The phase composition of the extracted rutin was verified by the XRD analysis and NMR measurements. It was found that 2.85% of rutin could be extracted from Filipendula ulmaria, which is 1.2 times higher than the results of similar studies. The biological activity of the isolated rutin was tested on rats. It was established in vivo that the extracted rutin normalizes blood glucose levels (glucose and glycosylated hemoglobin), insulin resistance (HOMA-IR index) and reduces the severity of dystrophic changes in the liver caused by high-fat and high-carbohydrate diets. The introduction of rutin corrects lipid profile indicators (triglycerides, cholesterol, cholesterol fractions in lipoproteins and atherogenic indices), cytolysis indicators of hepatocytes, and liver steatosis (ALT, AST/ALT, triglycerides). Thus, the novel source of rutin opens the possibility for a wide use of this flavonoid in the food technology and pharmaceutical industry. Full article

(This article belongs to the Section Medical Biotechnology)

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11 pages, 1224 KB

Open AccessArticle

Automation of Polysaccharide Quantification: A Rapid High-Throughput Assay Enabled by Liquid Handling Technology

by Samuel Nicacio, Winston Umakanth Balasundaram, Aboli Bhingarkar, Daniel Cho, Rashmi Ghayal, Anup Datta and Subhash V. Kapre

BioTech 2026, 15(1), 24; https://doi.org/10.3390/biotech15010024 - 20 Mar 2026

Abstract

Different methods are used today for polysaccharide quantitation, including HPLC and various colorimetric assays. Among these, the anthrone-sulfuric acid assay (anthrone assay) is popular when the sample matrix is suitable, such as in purified polysaccharides and monovalent bulk conjugate components of glycoconjugate vaccines. [...] Read more.

Different methods are used today for polysaccharide quantitation, including HPLC and various colorimetric assays. Among these, the anthrone-sulfuric acid assay (anthrone assay) is popular when the sample matrix is suitable, such as in purified polysaccharides and monovalent bulk conjugate components of glycoconjugate vaccines. While relatively safe, quick, and affordable, the anthrone assay requires significant operator time to complete and is not suited to high-throughput processing. Furthermore, the anthrone-sulfuric acid reagent presents a unique challenge to automation efforts due to its corrosive properties. Reported here is an automated anthrone assay via a liquid handling system (LHS). Twenty-three serotypes of pneumococcal (PNU) polysaccharide were quantified with the traditional anthrone assay and subsequently analyzed using the anthrone LHS method. The anthrone LHS method was evaluated for accuracy compared to the manual method and later validated according to ICH Q2 (R2) guidelines. To our knowledge, this is the first fully unattended and corrosion-mitigated anthrone assay validated under ICH Q2 (R2), capable of overnight batch operation. The developed assay can quantify polysaccharides with an accuracy of 81–115%, is precise to a coefficient of variation of <7.0%, and is linear between 30 and 650 µg/mL range (R² ≥ 0.993). The assay can process eight samples per hour, can be utilized in overnight operation, and completes all pipetting, incubation, and data export steps automatically. Full article

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24 pages, 1344 KB

Open AccessArticle

Co-Transfected Plasmids Enhance Transient Expression of Reporter Genes

by Shih-Yen Lo, Chee-Hing Yang, Yu-Ru Chan, Yi-Tzu Chao, Meng-Jiun Lai and Hui-Chun Li

BioTech 2026, 15(1), 23; https://doi.org/10.3390/biotech15010023 - 4 Mar 2026

Abstract

Transient DNA transfection is routinely used to study gene function and elucidate the regulation of biological pathways, and it is also widely applied in biotechnology for large-scale recombinant protein production. The results of recent studies involving mammalian cells have highlighted that competition for [...] Read more.

Transient DNA transfection is routinely used to study gene function and elucidate the regulation of biological pathways, and it is also widely applied in biotechnology for large-scale recombinant protein production. The results of recent studies involving mammalian cells have highlighted that competition for cellular resources during gene expression can bias data interpretation, directly affecting co-transfection experiments. In this study, our results showed that co-transfected plasmids markedly enhance transient—but not stable—expression of various reporter genes across different cell types. The enhancement of transient reporter gene expression by additional plasmid DNA occurs when these DNAs are co-delivered simultaneously and is unlikely to be mediated by cytokine induction. Furthermore, co-transfected plasmids were shown to upregulate transcription, but not translation, of the reporter gene during transient expression. Thus, the observed enhancement may result from competition between co-transfected plasmids and reporter constructs for cellular proteins that interact with transfected DNA, such as histones. Indeed, Pracinostat (SB939), an inhibitor of histone deacetylase, was able to enhance the transient expression of the reporter gene dose-dependently. Overall, this study provides insights that may facilitate improved transient expression of recombinant genes in biotechnological applications. Full article

(This article belongs to the Section Medical Biotechnology)

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17 pages, 7794 KB

Open AccessReview

Artificial Intelligence and Digital Technology in Cardiovascular Imaging: A Narrative Review

by Constantinos H. Papadopoulos, Dimitris Karelas, Christina Floropoulou, Konstantina Tzavida, Dimitrios Oikonomidis, Athanasios Tasoulis, Evangelos Tatsis, Ioannis Kouloulias and Nikolaos P. E. Kadoglou

BioTech 2026, 15(1), 22; https://doi.org/10.3390/biotech15010022 - 3 Mar 2026

Abstract

The rapid expansion of digital technologies and artificial intelligence (AI) has profoundly transformed cardiovascular imaging, enabling more precise, efficient, and reproducible assessment of cardiac structure and function. This narrative review summarizes recent advances in AI-driven methods across echocardiography, cardiac computed tomography, cardiac magnetic [...] Read more.

The rapid expansion of digital technologies and artificial intelligence (AI) has profoundly transformed cardiovascular imaging, enabling more precise, efficient, and reproducible assessment of cardiac structure and function. This narrative review summarizes recent advances in AI-driven methods across echocardiography, cardiac computed tomography, cardiac magnetic resonance, and nuclear imaging, with emphasis on image acquisition, automated quantification, and diagnostic and prognostic interpretation. We reviewed contemporary literature describing machine-learning and deep-learning applications for image reconstruction, segmentation, radiomics, and multimodal data integration. Current evidence demonstrates that AI improves image quality, reduces acquisition and analysis time, and enables automated, highly reproducible measurements of chamber volumes, function, tissue characterization, coronary anatomy, and myocardial perfusion, while facilitating advanced pattern recognition for differential diagnosis and risk stratification. Furthermore, digital platforms support remote acquisition, tele-echocardiography, and AI-assisted training of non-expert operators. Despite these advances, challenges remain regarding external validation, generalizability across vendors and populations, explainability, data governance, and regulatory compliance. In conclusion, AI and digital technologies are reshaping cardiovascular imaging by enhancing accuracy, efficiency, and accessibility, but their safe and effective clinical integration requires robust multicenter validation, transparent reporting, and ethical-legal frameworks that ensure trust, equity, and accountability. Full article

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

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18 pages, 3194 KB

Open AccessArticle

Engineering of Extracellular Vesicles for Targeted Delivery of Prodigiosin

by Ivan Guryanov, Sirina Sabirova, Svetlana Batasheva, Svetlana Konnova, Arthur Khannanov, Marianna Kutyreva and Ekaterina Naumenko

BioTech 2026, 15(1), 21; https://doi.org/10.3390/biotech15010021 - 1 Mar 2026

Abstract

The therapeutic potential of prodigiosin as a hydrophobic anticancer agent can be enhanced by various approaches, one of which is the loading of PG into extracellular vesicles. Drug distribution and stability in aqueous media play a crucial role in targeting and accumulation, thereby [...] Read more.

The therapeutic potential of prodigiosin as a hydrophobic anticancer agent can be enhanced by various approaches, one of which is the loading of PG into extracellular vesicles. Drug distribution and stability in aqueous media play a crucial role in targeting and accumulation, thereby enabling the attainment of therapeutically effective drug concentrations. Extracellular vesicles are nano-sized, cell-derived vesicles with a lipid bilayer membrane. Extracellular vesicles can be utilized as drug carriers for both water-soluble and non-water-soluble therapeutic agents. We hypothesized that microvesicles could effectively address the current challenges of prodigiosin delivery. Several different techniques have been developed for fabricating extracellular vesicles. These include microvesicles induction by cytochalasin B treatment as well as cell cultivation in serum depleted media. In our study, prodigiosin, like cytochalasin B, demonstrated efficacy in microvesicles formation based on protein quantification and Nanoparticle Tracking Analysis. In addition, Nanoparticle Tracking Analysis showed that vesicles from mesenchymal stem cells are more stable under ultrasound exposure. Microvesicles encapsulating prodigiosin, compared to unmodified naïve ones, demonstrated slightly increased zeta potentials and hydrodynamic diameters, which probably contributed to better stability. We demonstrated that ultrasonic treatment for the loading of prodigiosin does not significantly increase the proportion of prodigiosin-positive microvesicles in comparison with microvesicles induced with prodigiosin; moreover, this method cannot be considered as optimal due to its disadvantages, such as particle aggregation. Prodigiosin-induced and prodigiosin-loaded microvesicles from mesenchymal stem cells were significantly smaller and less polydisperse in size. Overall, prodigiosin encapsulated in extracellular vesicles might be more suitable for medical and clinical applications compared to pure forms of PG due to their cell membrane compatibility. Full article

(This article belongs to the Section Medical Biotechnology)

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28 pages, 5433 KB

Open AccessArticle

Predicting Protein–Protein Interactions by Convolutional Neural Network Model

by Shuaibo Shi, Ting Xiong, Dong Wang, Lingling Wei, Lin Li, Zhixin Li and Yanfen Lyu

BioTech 2026, 15(1), 20; https://doi.org/10.3390/biotech15010020 - 16 Feb 2026

Abstract

The study of protein–protein interactions (PPIs) is of significant importance for elucidating biological processes, clarifying pathological mechanisms, and promoting drug development. In this study, we proposed a method to predict PPIs based on protein sequence and gene sequence information, combined with convolutional neural [...] Read more.

The study of protein–protein interactions (PPIs) is of significant importance for elucidating biological processes, clarifying pathological mechanisms, and promoting drug development. In this study, we proposed a method to predict PPIs based on protein sequence and gene sequence information, combined with convolutional neural networks (CNNs). First, we extracted three types of features from protein sequence: global physicochemical properties features of the protein sequence, local same type of amino acid position variation features, and protein evolutionary conservation features; simultaneously, we extracted single nucleotide frequency and positional features, dinucleotide frequency features, and trinucleotide frequency features from the corresponding gene sequence. During the feature extraction process, we employed the amphiphilic pseudo amino acid composition (APAAC) method to extract the global hydrophobicity and hydrophilicity features of the protein sequence; we defined a new mathematical descriptor—

θ

interval deviation product factor—to extract protein evolutionary conservation features from Position Specific Scoring Matrix (PSSM); we also defined a mapping function to map all nucleotides in the gene sequence onto a unit circle, and then extracted nucleotide positional features from the mapped points. Second, based on extracted features, we constructed a 36 × 32 sample feature grayscale map to represent a protein pair sample. Finally, we developed a CNN model to predict PPIs. Our method achieved superior results on four species test sets: an accuracy of 99.28% on the Saccharomyces cerevisiae dataset, 98.15% on the Drosophila melanogaster dataset, 98.62% on the Homo sapiens dataset, and 96.84% on the Mus musculus dataset, outperforming existing computational methods. Furthermore, we extended the application of this method to the prediction of protein–protein interaction networks and non-interaction networks, and also achieved promising results. Full article

(This article belongs to the Section Computational Biology)

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13 pages, 885 KB

Open AccessArticle

Post-Inoculation Drying and Storage Effects on HAB Viability and Nutrient Retention in Biochar

by Christiana Bitrus, Ademola Hammed, Tawakalt Ayodele and Niloy Chandra Sarker

BioTech 2026, 15(1), 19; https://doi.org/10.3390/biotech15010019 - 12 Feb 2026

Abstract

Background/Objectives: The effects of thermal drying on the viability of beneficial microorganisms immobilized in biochar, as well as on biochar nutrient retention, remain insufficiently understood. This study aimed to evaluate how drying temperature influences the survival of hyper-ammonia-producing bacteria (HAB) immobilized on pine [...] Read more.

Background/Objectives: The effects of thermal drying on the viability of beneficial microorganisms immobilized in biochar, as well as on biochar nutrient retention, remain insufficiently understood. This study aimed to evaluate how drying temperature influences the survival of hyper-ammonia-producing bacteria (HAB) immobilized on pine wood biochar and to assess the impact of subsequent storage on bacterial recovery and nutrient stability. Methods: Biochar was inoculated with HAB and subjected to drying at temperatures ranging from 40 to 60 °C. Following drying, samples were characterized and stored for 30 days. Microbial revival was assessed through reculturing, while changes in surface functional groups were analyzed using FTIR spectroscopy. Nutrient retention, particularly nitrogen content, was also evaluated. Results: Higher drying temperatures resulted in reduced immediate microbial revival during reculturing. However, samples exhibiting limited immediate recovery demonstrated enhanced revival after the 30-day storage period. FTIR analysis revealed that drying temperature modified the availability of surface functional groups associated with microbial attachment and activity. Nutrient analysis indicated only minor reductions in nitrogen retention in biochar dried at temperatures above 55 °C. Conclusions: Drying temperature significantly affects both the short-term survival and post-storage recovery of beneficial microorganisms immobilized in biochar. While elevated temperatures may initially suppress microbial activity, recovery potential during storage remains substantial. Optimizing drying conditions is therefore essential to balance microbial viability with nutrient retention in biochar-based formulations. Full article

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20 pages, 5618 KB

Open AccessArticle

Transcriptomic Analysis Reveals an NRF2-Mediated Redox and Metabolic Reprogramming in Sorafenib-Resistant Hepatocellular Carcinoma Cells

by Angelo Michilli, Cristian Bassi, Farzaneh Moshiri, Bruno De Siena, Rosaria Marinaro, Elisa Callegari, Massimo Negrini and Silvia Sabbioni

BioTech 2026, 15(1), 18; https://doi.org/10.3390/biotech15010018 - 11 Feb 2026

Abstract

Despite the advent of immune checkpoint inhibitor-based regimens, sorafenib remains an important therapeutic option for patients with advanced hepatocellular carcinoma (HCC) who are ineligible for immunotherapy. However, its clinical efficacy is limited by the emergence of drug resistance, whose underlying molecular mechanisms remain [...] Read more.

Despite the advent of immune checkpoint inhibitor-based regimens, sorafenib remains an important therapeutic option for patients with advanced hepatocellular carcinoma (HCC) who are ineligible for immunotherapy. However, its clinical efficacy is limited by the emergence of drug resistance, whose underlying molecular mechanisms remain incompletely understood. To investigate these mechanisms, we established a murine model of acquired sorafenib resistance and performed comparative RNA sequencing of sorafenib-sensitive versus -resistant Hep55.1C hepatoma cells. Transcriptomic profiling revealed a distinct resistance-associated signature comprising 1264 significantly deregulated genes (adjusted p < 0.03, fold change > 3.0). Pathway analysis and Gene Set Enrichment Analyses (GSEA) indicated a coordinated downregulation of metabolic and intercellular signaling pathways, accompanied by marked upregulation of redox-regulatory, mitochondrial and cellular stress-response programs. Genes transcriptionally regulated by nuclear factor erythroid 2-related factor 2 (NRF2) including Gpx4, Txn1, Txnrd1, Hmox1, Fth1, Taldo1, Phgdh, and MafG, involved in antioxidant defense, ferroptosis suppression and metabolic rewiring, were all upregulated in resistant cells. Pharmacological inhibition of NRF2 activity using brusatol restored sensitivity to sorafenib, functionally implicating NRF2-dependent pathways in the maintenance of the resistant phenotype. These findings demonstrate that acquired sorafenib resistance in HCC is associated with a stable NRF2-driven transcriptional and metabolic reprogramming that enhances antioxidant capacity, suppresses ferroptosis and promotes tumor cell survival. Targeting NRF2-regulated redox metabolism may therefore represent a promising strategy to overcome therapeutic resistance in HCC. Full article

(This article belongs to the Special Issue BioTech: 5th Anniversary)

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32 pages, 3612 KB

Open AccessReview

Catching the Elusive Phytophthora: A Review of Methods and Applications for Pathogen Detection and Identification Across Agricultural, Horticultural, Forestry and Ornamental Settings

by Viola Papini, Alessandra Benigno, Domenico Rizzo and Salvatore Moricca

BioTech 2026, 15(1), 17; https://doi.org/10.3390/biotech15010017 - 9 Feb 2026

Abstract

Species of the genus Phytophthora are among the most detrimental plant pathogens globally, representing a significant threat to global agriculture, horticulture, and forestry. These zoosporic oomycetes have historically caused devastating outbreaks, including, just to mention a few, late blight of potato in Ireland; [...] Read more.

Species of the genus Phytophthora are among the most detrimental plant pathogens globally, representing a significant threat to global agriculture, horticulture, and forestry. These zoosporic oomycetes have historically caused devastating outbreaks, including, just to mention a few, late blight of potato in Ireland; jarrah dieback of eucalyptus in Western Australia; ink disease of chestnut in Europe; sudden oak death and sudden larch death of coast live oak and tanoak in the Western US, and of Japanese larch in the UK. The environmental and ecological impacts of the diseases they cause result in significant economic costs that often have social repercussions. With the acceleration of globalization, enhancing the movement of plant material, in particular with the global live plant trade, the spread of Phytophthora to new, uncontaminated territories has intensified. Nurseries play a key role in the movement of these pathogens, the trade of contaminated stocks representing their major dissemination route. However valuable, conventional detection techniques, including baiting and direct isolation, are too slow and labour-intensive to meet current diagnostic requirements, particularly given the huge volumes of plants traded globally. This problem becomes even more acute when large volumes of potentially infectious plant material need to be processed in a short time frame, as it is often necessary to provide accurate and timely responses to interested parties. Early and precise detection is thus vital to avert outbreaks and mitigate long-term consequences. This review evaluates and contrasts the efficacy of novel detection methods against traditional approaches, emphasizing their significance in managing the escalating threat posed by Phytophthora spp. worldwide. Despite technological advances, critical challenges remain that limit the reliability and large-scale adoption of new diagnostic methods. Research still needs to bridge the gap between the laboratory and the field in terms of accuracy, sensitivity and diagnostic costs. Recent innovations focus on sensor technology and point-of-care (POC) devices for faster, more sensitive, and low-cost specific detection of Phytophthora spp. in plant matrices, water and soil. Enhancing diagnostic capabilities through these tools is crucial for protecting agricultural productivity, local economies, and natural ecosystems. Full article

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

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34 pages, 3681 KB

Open AccessReview

Carboxylic Acid Production from Organic Waste: Integrating Substrate Composition, Reactor Configuration, Inoculum, and Future Perspectives

by Ajay Thapa, Shiyu Fu, Joseph Sebastian, Onita Basu, Farah Hosseinian, Utsav Sharma, Dayanand Sharma and Abid Hussain

BioTech 2026, 15(1), 16; https://doi.org/10.3390/biotech15010016 - 9 Feb 2026

Abstract

Acidogenic fermentation is a promising biotechnology for converting organic wastes into carboxylic acid (CA), which has significant commercial value and diverse applications in the food, chemical, pharmaceutical, and cosmetic industries. However, major challenges such as limited substrate hydrolysis and lower CA production hinder [...] Read more.

Acidogenic fermentation is a promising biotechnology for converting organic wastes into carboxylic acid (CA), which has significant commercial value and diverse applications in the food, chemical, pharmaceutical, and cosmetic industries. However, major challenges such as limited substrate hydrolysis and lower CA production hinder further development of this biotechnology towards full-scale implementation. This review provides a comprehensive overview of the current status of acidogenic fermentation, focusing on substrate composition, inoculum, and reactor design, along with potential strategies to overcome reactor-specific limitations and enhance CA production. It was found that the substrate composition, particularly its carbohydrate, protein, and lipid contents, strongly influences both CA production and yield. Specifically, carbohydrate-rich substrates yield higher CA production compared to protein- and lipid-rich substrates. These substrates have been investigated in different reactor configurations for CA production. Among them, the leachate bed reactor and anaerobic membrane bioreactor have demonstrated superior performance, achieving higher CA production with acetic and butyric acids as the dominant CA composition. These reactors are generally operated using three types of inocula: aerobic and anaerobic inoculum, enriched inoculum, and rumen microorganisms. Interestingly, rumen microorganisms are effective in degrading complex substrates, whereas enriched inoculum accelerates hydrolysis and acidogenesis processes within a shorter fermentation time. The findings presented herein will provide valuable information for addressing the challenges associated with acidogenic fermentation and lay the foundation for future research aimed at upscaling this biotechnology to a commercial scale. Full article

(This article belongs to the Section Environmental Biotechnology)

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14 pages, 1679 KB

Open AccessArticle

Functional Analysis of the NinaB-like Gene in Body Color Regulation of Neocaridina denticulata sinensis

by Haifan Li, Lili Zhang, Guodong Wang and Tanjun Zhao

BioTech 2026, 15(1), 15; https://doi.org/10.3390/biotech15010015 - 5 Feb 2026

Abstract

Carotenoid-based pigmentation is crucial for the ornamental and commercial value of the cherry shrimp (Neocaridina denticulata sinensis). While several genes are known to influence carotenoid metabolism, the genetic basis for specific color strains remains largely unexplored. Here, we functionally characterized NinaB-like [...] Read more.

Carotenoid-based pigmentation is crucial for the ornamental and commercial value of the cherry shrimp (Neocaridina denticulata sinensis). While several genes are known to influence carotenoid metabolism, the genetic basis for specific color strains remains largely unexplored. Here, we functionally characterized NinaB-like, a homolog of a carotenoid oxygenase, in cherry shrimp pigmentation. We employed qPCR to gain gene expression profiles, utilized RNAi technology to analysize the relation between its expression level and carotenoid accumulation, and performed GT-seq to identify genotypes of different color strains. Significant differential expression of NinaB-like was observed not only across distinct color strains but also during embryonic development of cherry shrimp (p < 0.05), peaking at the red strain and post-larval stage of cherry shrimp. RNA interference-mediated knockdown of NinaB-like resulted in a marked increase in red pigment deposition at the metanauplius and pre-zoea stages, confirming its role as a negative regulator of carotenoid accumulation. Importantly, we identified two tightly linked, non-synonymous SNPs (927C > A and 935A > C) within the NinaB-like coding region that exhibited a strong association with body color. Our study provides the first functional evidence that NinaB-like is a negative regulator of carotenoid degradation and a major genetic determinant for body color in cherry shrimp, providing new insights for genetic breeding and biological research. Full article

(This article belongs to the Section Biotechnology Regulation)

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10 pages, 1874 KB

Open AccessArticle

Plant-Derived Hydrolysates Are a Suitable Replacement for Tryptone N1 in Recombinant Protein Expression Using Human Embryonic Kidney (HEK293-6E) Cells

by Shafqat Shabir, Md. Shahadat Hossain, Lucie Egly, Gizem Yalkin and Franco H. Falcone

BioTech 2026, 15(1), 14; https://doi.org/10.3390/biotech15010014 - 5 Feb 2026

Abstract

Human embryonic kidney (HEK293) cells are a widespread choice for recombinant protein expression. To optimise yields, the hydrolysate Tryptone N1 (TN1) is commonly added post-transfection. TN1 is obtained by controlled enzymatic digestion of casein. As an animal by-product, TN1 faces stricter regulations during [...] Read more.

Human embryonic kidney (HEK293) cells are a widespread choice for recombinant protein expression. To optimise yields, the hydrolysate Tryptone N1 (TN1) is commonly added post-transfection. TN1 is obtained by controlled enzymatic digestion of casein. As an animal by-product, TN1 faces stricter regulations during cross-country shipments than plant-based products. This raises the question of whether plant-derived peptides are a suitable alternative to TN1. Using polyethyleneimine (PEI) as a cationic polymer, we transfected HEK293-6E cells grown in suspension in serum-free medium and divided the transfectants into four groups (each in triplicate). Two plant-based hydrolysates each derived from pea and broad bean were compared with TN1 and a no-hydrolysate control group. We monitored the cultures for total cell numbers and viability at days 1, 4, and 5 post-transfection. Both plant-based hydrolysates and TN1 showed similar live cell percentages, in contrast to the no-hydrolysate control, which showed lower viability. Five days post-transfection, the expressed His-tagged protein, a tegumental antigen from the eukaryotic parasite Echinococcus granulosus, was retrieved from the serum-free culture supernatant, and the expressed recombinant protein was quantified. The linear ranges for the protein load on the stain-free blot and for the use of the fluorescent anti-His-Tag Alexa₄₈₈ antibody were determined. Using these parameters, stain-free Western blotting and total protein normalization were performed. The plant-derived pea and broad bean hydrolysates reproducibly resulted in similar expression levels as animal-derived TN1; all three hydrolysates were better than no hydrolysate. We conclude that plant-derived hydrolysates are a suitable, more sustainable replacement for TN1. Full article

(This article belongs to the Section Medical Biotechnology)

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17 pages, 1665 KB

Open AccessArticle

CRISPR/Cas9-Mediated Knockout of OsHSBP1 Confers Heat Tolerance to Bacthom 7 Elite Rice Cultivar

by Phuong Duy Nguyen, Van Thi Pham, Ha Thanh Nguyen, Khoa Dang Dang, Tu Tuan Tran, Dai Lan Tran, Thanh Duc Nguyen, Thao Duc Le, Xuan Hoi Pham, Xuan Dang Tran and Quyen Le Cao

BioTech 2026, 15(1), 13; https://doi.org/10.3390/biotech15010013 - 4 Feb 2026

Abstract

This study investigates the functional role of OsHSBP1, a heat shock factor-binding protein, in regulating abiotic stress tolerance in rice, with the aim of enhancing climate resilience in the elite indica cultivar Bacthom 7 (BT7). Using Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated [...] Read more.

This study investigates the functional role of OsHSBP1, a heat shock factor-binding protein, in regulating abiotic stress tolerance in rice, with the aim of enhancing climate resilience in the elite indica cultivar Bacthom 7 (BT7). Using Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR/Cas9) genome editing, we generated transgene-free homozygous knockout lines targeting OsHSBP1 and evaluated their physiological, biochemical, and agronomic responses under heat stress. Mutant lines exhibited markedly improved tolerance to both stresses, with survival rates reaching 43–46% under heat stress, compared to near-zero in wildtype plants. Enhanced tolerance was associated with significantly increased catalase and peroxidase activities and reduced oxidative damage, including lower malondialdehyde content and decreased superoxide accumulation. Despite these stress-related advantages, the knockout lines showed minimal differences in key agronomic traits under normal growing conditions, with comparable plant height, tillering ability, grain yield, and amylose content relative to the wildtype. These results demonstrate that OsHSBP1 functions as a negative regulator of abiotic stress tolerance in rice, and its knockout enhances resilience without compromising yield potential. The study highlights OsHSBP1 as a promising target for precision breeding of climate-resilient rice cultivars. Full article

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

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22 pages, 7755 KB

Open AccessArticle

Transcriptomic Insights into lncRNA–miRNA–mRNA Networks Regulating Angiogenesis and Metastasis in Prostate Cancer

by Jonathan Puente-Rivera, Stephanie I. Nuñez Olvera, Ameyatzin Ereth Robles-Chávez, Nayeli Goreti Nieto-Velázquez and María Elizbeth Alvarez-Sánchez

BioTech 2026, 15(1), 12; https://doi.org/10.3390/biotech15010012 - 1 Feb 2026

Abstract

Prostate cancer (PCa) is a leading cause of cancer-related mortality in men and is often characterized by aggressive growth and bone metastasis. Angiogenesis plays a central role in tumor progression and dissemination. This study aimed to explore the regulatory roles of long non-coding [...] Read more.

Prostate cancer (PCa) is a leading cause of cancer-related mortality in men and is often characterized by aggressive growth and bone metastasis. Angiogenesis plays a central role in tumor progression and dissemination. This study aimed to explore the regulatory roles of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) in angiogenesis and metastasis during PCa progression. Publicly available RNA-seq datasets were analyzed to identify differentially expressed miRNAs between metastatic (N1) and nonmetastatic (N0) PCa. Bioinformatic tools were used to reconstruct co-regulatory networks involving miRNAs, lncRNAs, and angiogenesis-related mRNAs. RT-qPCR was performed on serum-derived liquid biopsies from N0 and N1 patients and healthy controls to validate the key regulatory axes. Transcriptomic analysis revealed that miRNAs such as hsa-miR-183-5p and hsa-miR-216a-5p were upregulated in N1 PCa and associated with pro-angiogenic signaling, whereas hsa-miR-206 and hsa-miR-184, known for their anti-angiogenic functions, were downregulated. Network analysis identified the LINC00261–miR-206–HIF1A axis as the central regulatory module. RT-qPCR validation confirmed the significant downregulation of LINC00261 and miR-206, along with HIF1A overexpression in N1 samples compared to N0 and controls (p < 0.001), supporting in silico predictions. These findings highlight the role of ncRNA-mediated regulation of PCa angiogenesis and metastasis. The LINC00261–miR-206–HIF1A axis may serve as a promising noninvasive biomarker and potential therapeutic target. The integration of computational and experimental data provides a strong rationale for the further functional validation of advanced PCa. Full article

(This article belongs to the Special Issue Integrative Omics Approaches for Precision Biotech: Tools, Applications and Future Perspectives)

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