BioTech

13 pages, 3654 KB

Open AccessArticle

Structure-Based Pipeline for Plant Enzymes: Pilot Study Identifying Novel Ginsenoside Biosynthetic UGTs

by Kisook Jung, Ick-hyun Jo, Bae Young Choi and Jaewook Kim

BioTech 2025, 14(3), 73; https://doi.org/10.3390/biotech14030073 - 12 Sep 2025

Models that predict the 3D structure of proteins enable us to easily analyze the structure of unknown proteins. Though many of these models have been found to be accurate, their application in plant proteins is not always entirely accurate. Thus, we aimed to [...] Read more.

Models that predict the 3D structure of proteins enable us to easily analyze the structure of unknown proteins. Though many of these models have been found to be accurate, their application in plant proteins is not always entirely accurate. Thus, we aimed to develop a versatile yet simple pipeline that can predict novel proteins with a specific function. As an example, via benchmark studies, we sought to discover novel UDP-glycosyltransferases (UGTs) potentially involved in ginsenoside biosynthesis. Since the functionality of these UGTs has been shown to be determined by a few amino acids, a 3D-structure-based pipeline was required. Our pipeline includes four sequential steps: a sequence-based homology search, AlphaFold3-based 3D structure prediction, docking simulations with ginsenoside intermediates using SwissDock and CB-Dock2, and MPEK analysis to assess interaction stability. Through the application of this benchmark, we optimized the role of each module in the pipeline and successfully identified four novel UGT candidates. These candidates are predicted to catalyze the conversion of protopanaxadiol (PPD) to compound K (CK) or protopanaxatriol (PPT) to ginsenoside F1. This pilot study demonstrates how our pipeline can be used for the functional annotation of plant proteins and the discovery of enzymes involved in specialized pathways. Full article

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

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24 pages, 6086 KB

Open AccessArticle

Benchmarking the Base Randomization Algorithm as a Possible Tool for the Initial Step of Generating a Virtual RNA Aptamers Library

by Kabelo P. Mokgopa, Shina D. Oloniiju, Kevin A. Lobb and Tendamudzimu Tshiwawa

BioTech 2025, 14(3), 72; https://doi.org/10.3390/biotech14030072 - 12 Sep 2025

Abstract

While databases are emerging across various domains, from small molecules to genomics and proteins, aptamer databases remain scarce, if not entirely absent. Such databases could serve as a comprehensive resource for advancing research, innovation, and the applications of aptamer technology across multiple fields. [...] Read more.

While databases are emerging across various domains, from small molecules to genomics and proteins, aptamer databases remain scarce, if not entirely absent. Such databases could serve as a comprehensive resource for advancing research, innovation, and the applications of aptamer technology across multiple fields. This advancement would likely lead to improvements in healthcare, environmental monitoring, and biotechnology. Furthermore, the establishment of aptamer databases would facilitate molecular modelling and machine learning, opening doors to further advancements in understanding and utilizing aptamers. Against this backdrop, in this study, we present and benchmark the Base Randomization Algorithm (BRA) as a potential solution to the scarcity of aptamer databases. Through statistical analysis, we examine key factors such as minimum free energy (MFE), base compositions, and base arrangements. Notably, sequences generated using the BRA exhibit a Gaussian distribution pattern. We also examine the details of how each base within a sequence is chosen using mathematical principles, ensuring that the sequences are valid and optimized statistically. Additionally, we explore how the length of the randomized generated sequences can affect the folding of their structures at both the secondary and tertiary levels. Based on composition analysis, we propose that the base mean of the dataset can be approximated as

{\bar{x}}_{B} \approx P (x) \times N

, for dataset of sequences with the same length and

{\bar{x}}_{B} \approx P (x) \times M,

where

M

is the median and

N

the mean, for a dataset with randomized length that follows a Gaussian distribution. Full article

(This article belongs to the Section Computational Biology)

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21 pages, 4549 KB

Open AccessArticle

Dual Role of Tenebrio molitor Frass in Sustainable Agriculture: Effects on Free-Living Nematodes and Suppression of Meloidogyne incognita

by Evgenia Rizou, Nikolaos Monokrousos, Triantafyllia Kardami, Georgia V. Baliota, Christos I. Rumbos, Christos G. Athanassiou, Nikolaos Tsiropoulos and Nikoletta Ntalli

BioTech 2025, 14(3), 71; https://doi.org/10.3390/biotech14030071 - 8 Sep 2025

Abstract

Insect-derived frass is gaining attention as a circular bioeconomy product with fertilizing and pest-suppressive potential. This study investigates Tenebrio molitor frass as a soil amendment for promoting beneficial nematodes and suppressing Meloidogyne incognita. A 40-day pot experiment on clay loam soil tested [...] Read more.

Insect-derived frass is gaining attention as a circular bioeconomy product with fertilizing and pest-suppressive potential. This study investigates Tenebrio molitor frass as a soil amendment for promoting beneficial nematodes and suppressing Meloidogyne incognita. A 40-day pot experiment on clay loam soil tested with six inputs: raw and heat-treated frass (0.5%, 1% w/w), Melia azedarach fruit powder (1.6%), and an untreated control. Soil nematode communities were assessed at 5 and 40 days after application (DAA), and nematicidal activity was evaluated in vitro. Raw frass at 1% induced a rapid response from free-living nematodes at 5 DAA, with increased abundance of bacterivorous taxa such as Rhabditis and Acrobeloides, alongside a higher Enrichment Index (EI), indicating short-term nutrient availability. At 40 DAA, only 1% raw frass consistently supported more cp-1 bacterivores and slightly increased Shannon diversity. Network analysis revealed more connected, modular structures in raw frass treatments, suggesting enhanced food web complexity. However, omnivore and predator effects were limited. Raw frass extracts caused over 80% paralysis of Meloidogyne incognita juveniles within 24 h, significantly outperforming heat-treated frass and Melia extracts. T. molitor frass moderately stimulates opportunistic nematodes and provides strong nematicidal effects, supporting its potential as a multifunctional input for sustainable soil management. Full article

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

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23 pages, 4560 KB

Open AccessArticle

A Single-Nucleus Transcriptomic Atlas of the Mouse Lumbar Spinal Cord: Functional Implications of Non-Coding RNAs

by Pablo Ruiz-Amezcua, Miguel Nieto Hernández, Javier García Flores, Clara Plaza Alonso, David Reigada, Teresa Muñoz-Galdeano, Eva Vargas, Rodrigo M. Maza, Francisco J. Esteban and Manuel Nieto-Díaz

BioTech 2025, 14(3), 70; https://doi.org/10.3390/biotech14030070 - 3 Sep 2025

Abstract

The adult lumbar spinal cord plays a critical role in locomotor control and somatosensory integration, whose transcriptional architecture under physiological conditions has been characterized in various studies with restricted numbers of individuals (up to four). Here, we present an integrative single-nucleus RNA sequencing [...] Read more.

The adult lumbar spinal cord plays a critical role in locomotor control and somatosensory integration, whose transcriptional architecture under physiological conditions has been characterized in various studies with restricted numbers of individuals (up to four). Here, we present an integrative single-nucleus RNA sequencing (snRNA-seq) atlas of the healthy adult mouse lumbar spinal cord, assembled from over 86,000 nuclei from 16 samples across five public datasets. Using a harmonized computational pipeline, we identify all major spinal cell lineages and resolve 17 transcriptionally distinct neuronal subtypes. A central novelty of our approach is the systematic inclusion of non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs) and pseudogenes. By comparing transcriptomic analyses based on coding-only, non-coding-only, and combined gene sets, we show that ncRNAs, despite accounting to a 10% of the recorded information of each cell, contribute to cell type-specific signatures. This resource offers a high-resolution, ncRNA-inclusive reference for the adult spinal cord and provides a foundation for future studies on spinal plasticity, injury, and regeneration. Full article

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

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13 pages, 486 KB

Open AccessArticle

Effect of Selected Truffle-Associated Bacteria and Fungi on the Mycorrhization of Quercus ilex Seedlings with Tuber melanosporum

by Eva Gómez-Molina, Pedro Marco, Sergi Garcia-Barreda, Vicente González and Sergio Sánchez

BioTech 2025, 14(3), 69; https://doi.org/10.3390/biotech14030069 - 1 Sep 2025

Abstract

The success of truffle cultivation is especially dependent on the quality of truffle-mycorrhized seedlings, which are typically produced in nurseries under aseptic conditions to avoid root colonization by undesired ectomycorrhizal fungi. However, such practices may also eliminate beneficial microorganisms that could support truffle [...] Read more.

The success of truffle cultivation is especially dependent on the quality of truffle-mycorrhized seedlings, which are typically produced in nurseries under aseptic conditions to avoid root colonization by undesired ectomycorrhizal fungi. However, such practices may also eliminate beneficial microorganisms that could support truffle symbiosis and improve seedling quality. In this study, twelve endophytic bacterial and fungal strains, isolated from the Tuber melanosporum environment (gleba tissue, mycorrhizae and truffle brûlé), were tested for their effect on T. melanosporum mycorrhization levels in inoculated Quercus ilex seedlings under nursery conditions. Co-inoculation with a strain of Agrobacterium tumefaciens significantly enhanced root colonization by T. melanosporum, supporting its potential role as mycorrhizal helper bacterium. In contrast, a strain of Trichoderma harzianum negatively affected mycorrhization. The remaining strains did not show significant effects on seedling mycorrhization or seedling growth. Our findings support the hypothesis that specific bacterial strains associated with truffles can act as mycorrhizal helper bacteria, highlighting the potential for co-inoculation strategies to enhance quality of truffle-inoculated seedlings in nurseries. However, further research is needed to gain a deeper understanding of the interactions within the mycorrhizosphere that could contribute to improving nursery seedling quality. Full article

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

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18 pages, 1541 KB

Open AccessArticle

Organic Acid Production by Basfia succiniciproducens from Agro-Industrial By-Products

by Márta Balázs, Izabella Péter, Hunor Bartos, Zsolt Bodor, Emőke Antal, Csilla Albert and Ildikó Miklóssy

BioTech 2025, 14(3), 68; https://doi.org/10.3390/biotech14030068 - 1 Sep 2025

Abstract

A continuous effort is needed to develop sustainable production methods for industrial platform chemicals. B. succiniciproducens, a natural succinic acid-producer, can metabolize five and six carbon atoms containing sugars in pure form as well as from agro-industrial wastes. In our work, we [...] Read more.

A continuous effort is needed to develop sustainable production methods for industrial platform chemicals. B. succiniciproducens, a natural succinic acid-producer, can metabolize five and six carbon atoms containing sugars in pure form as well as from agro-industrial wastes. In our work, we investigate the conversion of industrial by-products, apple pomace from apple juice production, and whey waste from milk processing to succinic acid and other organic acids (lactic, formic, and acetic acid). We obtained a succinic acid yield of 0.224 g/g total consumed fermentable sugars, lactic acid yield was 0.087 g/g, in turn, formic acid was produced at a 0.034 g/g yield, and acetic acid was obtained at 0.010 g/g total consumed fermentable sugars, using a thermal pretreated apple pomace-based medium. In the case of pretreated whey-based medium formulation, we obtained a succinic acid yield of 0.236 g/g consumed lactose, while formic acid and acetic acid were produced as well (0.09 g/g and 0.101 g/g, respectively). We demonstrate that lactose is a promising carbon source for organic acid production by B. succiniciproducens, while our study is the first to propose the use of a similarly available agro-industrial by-product, apple pomace, for the fermentative production of succinic acid by B. succiniciproducens. Full article

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

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20 pages, 2741 KB

Open AccessArticle

Changes in Microbial Communities in Industrial Anaerobic Digestion of Dairy Manure Caused by Caldicellulosiruptor Pretreatment

by Jakob Young, Maliea Nipko, Spencer Butterfield and Zachary Aanderud

BioTech 2025, 14(3), 67; https://doi.org/10.3390/biotech14030067 - 28 Aug 2025

Abstract

Extremophilic biological process (EBP) pretreatment increases substrate availability in anaerobic digestion, but the effect on downstream microbial community composition in industrial systems is not characterized. Changes in microbial communities were determined at an industrial facility processing dairy manure in a modified split-stream system [...] Read more.

Extremophilic biological process (EBP) pretreatment increases substrate availability in anaerobic digestion, but the effect on downstream microbial community composition in industrial systems is not characterized. Changes in microbial communities were determined at an industrial facility processing dairy manure in a modified split-stream system with three reactor types: (1) EBP tanks at 70–72 °C; (2) mesophilic Continuously Stirred Tank Reactors (CSTRs); (3) mesophilic Induced Bed Reactors (IBRs) receiving combined CSTR and EBP effluent. All reactors had a two-day hydraulic retention time. Samples were collected weekly for 60 days. pH, volatile fatty acid and bicarbonate concentrations, COD, and methane yield were measured to assess tank environmental conditions. Microbial community compositions were obtained via 16S rRNA gene sequencing. EBP pretreatment increased acetate availability but led to a decline in the relative abundance of acetoclastic Methanosarcina species in downstream IBRs. Rather, syntrophic methanogens, e.g., members of Methanobacteriaceae, increased in relative abundance and became central to microbial co-occurrence networks, particularly in association with hydrogen-producing bacteria. Network analysis also demonstrated that these syntrophic relationships were tightly coordinated in pretreated digestate but absent in the untreated CSTRs. By promoting syntrophic methanogenesis while increasing acetate concentrations, EBP pretreatment requires system configurations that enable acetoclast retention to prevent acetate underutilization and maximize methane yields. Full article

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

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18 pages, 4748 KB

Open AccessArticle

Enhanced Bacterial Cellulose Production Using Hempseed Meal: Optimal Conditions and Properties

by Sawichaya Orpool, Suthaphat Kamthai, Thanyaporn Siriwoharn, Patompong Khaw-on, Aree Deenu and Srisuwan Naruenartwongsakul

BioTech 2025, 14(3), 66; https://doi.org/10.3390/biotech14030066 - 27 Aug 2025

Abstract

Hemp (Cannabis sativa L.) seed is progressively emerging as an innovative and sustainable source of plant oil. Defatted hempseed meal is rich in protein and carbohydrates, which bacteria can convert into cellulose using glucose and fructose. The optimal conditions for bacterial cellulose [...] Read more.

Hemp (Cannabis sativa L.) seed is progressively emerging as an innovative and sustainable source of plant oil. Defatted hempseed meal is rich in protein and carbohydrates, which bacteria can convert into cellulose using glucose and fructose. The optimal conditions for bacterial cellulose (BC) production from hempseed meal were evaluated by investigating total solid concentrations ranging from 8 to 16 °Brix using Komagataeibacter nataicola under controlled conditions. The changes in pH, bioactive compounds, organic acids, and carbon source concentrations were monitored during the fermentation process. The highest yield of BC, 12.41 g/L, was obtained at 10 °Brix after 14 days of fermentation. It was found that the production of BC was negatively impacted by a decrease in pH and an increase in organic acids. BC exhibited a ribbon-like 3D network structure and a crystallinity index of about 70%, with excellent water-holding capacity, low oil-holding capacity, high emulsifying activity, and high emulsion stability (11.21%, 2.71%, 34.33%, and 39.11%, respectively). This BC possesses exceptional mechanical properties, a high degree of crystallinity, and superior water-holding capacity, making it valuable in various industries such as food, pharmaceuticals, and biotechnology. Full article

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

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12 pages, 943 KB

Open AccessReview

Biomaterials and Tissue Engineering in Neurosurgery: Current Innovations and Future Directions

by Jagoš Golubović and Damjan Vučurović

BioTech 2025, 14(3), 65; https://doi.org/10.3390/biotech14030065 - 26 Aug 2025

Abstract

Neurosurgery is undergoing a significant transformation driven by advances in biomaterials and tissue engineering. These interdisciplinary innovations address challenges in repairing and regenerating neural tissues, integrating cranial and spinal implants, and improving patient outcomes. The incidence of neurological injuries such as traumatic brain [...] Read more.

Neurosurgery is undergoing a significant transformation driven by advances in biomaterials and tissue engineering. These interdisciplinary innovations address challenges in repairing and regenerating neural tissues, integrating cranial and spinal implants, and improving patient outcomes. The incidence of neurological injuries such as traumatic brain injury and spinal cord injury remains high, underscoring the need for improved therapeutic strategies. This review provides a comprehensive overview of current biomaterial and tissue engineering approaches in neurosurgery, highlighting developments in neural tissue repair, cranial and spinal implants, spinal cord injury treatment, and peripheral nerve regeneration. Key challenges—such as ensuring biocompatibility, modulating the immune response, and bridging the gap between laboratory research and clinical application—are discussed. Emerging technologies including 3D bioprinting, nanotechnology (removing microfluidics), and microfluidics are examined for their potential to revolutionize neurosurgical treatments. The need for interdisciplinary collaboration among neurosurgeons, material scientists, and biologists is emphasized as critical for overcoming translational barriers and accelerating the clinical translation of these promising technologies. Full article

(This article belongs to the Section Medical Biotechnology)

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10 pages, 1319 KB

Open AccessArticle

Translocation of Insecticidal Bt Protein in Transgrafted Plants

by Arisa Ando, Hitomi Ohkubo, Hisae Maki, Takumi Nishiuchi, Takumi Ogawa, Tomofumi Mochizuki, Daisaku Ohta, Hiroaki Kodama and Taira Miyahara

BioTech 2025, 14(3), 64; https://doi.org/10.3390/biotech14030064 - 25 Aug 2025

Abstract

Transgrafting constitutes a technique involving the integration of genetically modified (GM) and non-GM plant organisms. Typically, edible components derived from non-GM scions are categorized as non-GM food products, attributed to the absence of exogenous genetic material within their respective genomes. Non-GM food status [...] Read more.

Transgrafting constitutes a technique involving the integration of genetically modified (GM) and non-GM plant organisms. Typically, edible components derived from non-GM scions are categorized as non-GM food products, attributed to the absence of exogenous genetic material within their respective genomes. Non-GM food status could be compromised if proteins translocated across the graft interface. We investigated the movement of insecticidal Bacillus thuringiensis (Bt) crystal proteins, widely utilized in GM crop species. Tobacco plants engineered to express the Cry1Ab gene exhibited trace levels of Cry1Ab protein accumulation. In transgrafted plants, translocated Cry1Ab protein originating from GM rootstocks was detectable within scion foliar tissues but not within the seeds obtained from the non-GM scion. This result unequivocally demonstrates the capacity for Bt protein translocation from rootstocks to scions yet indicates a constrained distribution confined to scion tissues relatively close to the graft junction. While regulatory considerations necessitate a thorough appraisal of potential risks associated with Bt proteins, the results shown here facilitate the commercialization of the edible components as non-GM food products. Full article

(This article belongs to the Section Biotechnology Regulation)

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15 pages, 1726 KB

Open AccessArticle

Enhancing In Vitro Regeneration in Three Sweet Potato Genotypes: Interplay Between Disinfectant, Explant Age, and Genotype

by El Hadj Hussein Tapily, Kan Modeste Kouassi, Marius Konan Kouassi, John Steven S. Seka, Fidèle Tiendrébéogo and Justin S. Pita

BioTech 2025, 14(3), 63; https://doi.org/10.3390/biotech14030063 - 19 Aug 2025

Abstract

Regenerating sweet potato from field-derived plant material requires careful management of several critical factors, including the effectiveness of the disinfectant, the age of the explant, and the genotype used. In this context, establishing a reliable aseptic protocol is essential for successful in vitro [...] Read more.

Regenerating sweet potato from field-derived plant material requires careful management of several critical factors, including the effectiveness of the disinfectant, the age of the explant, and the genotype used. In this context, establishing a reliable aseptic protocol is essential for successful in vitro culture. This study aimed to assess the effects of two disinfectants (sodium hypochlorite and mercuric chloride), three sweet potato genotypes (Nakabo, Boyapleu, and Irene), and three explant ages (2, 3, and 4 weeks) on clean culture establishment and regeneration efficiency from nodal explants. The findings revealed that regeneration success is significantly influenced by the type and concentration of disinfectant, explant age, and genotype. Treatment with 10% sodium hypochlorite markedly reduced contamination, achieving clean culture and regeneration rates of 75.72 ± 3.36% and 86.83 ± 3.02%, respectively, regardless of explant age. In contrast, higher concentrations of mercuric chloride induced necrosis in the explants. The highest clean culture rate (93.82 ± 1.16%) was observed in 3-week-old explants, which also showed a regeneration rate of 54.93 ± 3.19%. Furthermore, the Boyapleu and Irene genotypes demonstrated good suitability for in vitro culture, whereas the Nakabo genotype performed poorly under the tested conditions. Full article

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

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16 pages, 2083 KB

Open AccessArticle

Effects of Glycerol and Phenolics on Myceliophthora heterothallica Endoxylanase Expressed in K. phaffii

by Jéssica de Araujo Zanoni, Izabela Karolina Costa Zilli, Guilherme de Paula Pretto, Flavio Augusto Vicente Seixas, Marcela Marques de Freitas Lima, Eliana Gertrudes de Macedo Lemos, Eleni Gomes, Gabriel Zazeri and Gustavo Orlando Bonilla-Rodriguez

BioTech 2025, 14(3), 62; https://doi.org/10.3390/biotech14030062 - 18 Aug 2025

Abstract

Industrial applications of xylanases in high-temperature settings are limited by enzyme instability. This study evaluated glycerol and phenolic compounds as modulators of the catalytic and structural properties of a recombinant Myceliophthora heterothallica endoxylanase (rMhXyn) expressed in Komagataella phaffii. Glycerol (20% v/ [...] Read more.

Industrial applications of xylanases in high-temperature settings are limited by enzyme instability. This study evaluated glycerol and phenolic compounds as modulators of the catalytic and structural properties of a recombinant Myceliophthora heterothallica endoxylanase (rMhXyn) expressed in Komagataella phaffii. Glycerol (20% v/v) significantly improved thermostability (5-fold increase in half-life at 55 °C), decreased the activation energy for catalysis, and enhanced structural rigidity as evidenced by molecular dynamics simulations (reduced RMSD and Rg). In contrast, phenolic acids provided only short-term stabilization at moderate temperatures and did not confer structural benefits. Enzyme kinetics revealed that glycerol enhanced catalytic turnover (↑V_max), while phenolic compounds modified both K′ and cooperativity (Hill coefficient). Thermodynamic analysis supported glycerol’s stabilizing effect, with increased ∆H_(D) and a positive shift in ∆S_(D). These results suggest glycerol as a superior stabilizer for rMhXyn in high-temperature bioprocesses such as lignocellulosic biomass hydrolysis. These findings highlight the potential of targeted additives to improve enzyme performance for biotechnological applications. Full article

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18 pages, 1363 KB

Open AccessArticle

Rosemary Extract: Phytochemical Composition and Potential for Eliminating Polymicrobial Biofilm of Candida albicans and Multidrug-Resistant Bacteria

by Tuana Mendonça Faria Cintra, Raquel Teles de Menezes, Lara Steffany de Carvalho, Leticia de Miguel Nazario, Leandro Wang Hantao, Maria Cristina Marcucci, Luciane Dias de Oliveira and Vanessa Marques Meccatti-Domiciano

BioTech 2025, 14(3), 61; https://doi.org/10.3390/biotech14030061 - 13 Aug 2025

Abstract

Herbal medicines can be promising for the treatment of infections caused by multidrug-resistant microorganisms. This study aimed to evaluate Rosmarinus officinalis (Rosemary) hydroalcoholic extract (RHE) regarding its phytochemical composition and potential for eliminating polymicrobial biofilm of Candida albicans with multidrug-resistant bacteria (Acinetobacter [...] Read more.

Herbal medicines can be promising for the treatment of infections caused by multidrug-resistant microorganisms. This study aimed to evaluate Rosmarinus officinalis (Rosemary) hydroalcoholic extract (RHE) regarding its phytochemical composition and potential for eliminating polymicrobial biofilm of Candida albicans with multidrug-resistant bacteria (Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa). The extraction and quantification of the extract (flavonoids and phenols) were performed, and its antioxidant activity (DPPH) and the presence of bio-active compounds were investigated using high-performance liquid chromatography with Diode Array Detection (HPLC-DAD) and Gas Chromatography–Mass Spectrometry (GC-MS). The minimum inhibitory concentration (MIC) and minimum microbicidal concentration (MMC) were determined, and the extract’s action on polymicrobial biofilms was evaluated using the MTT assay. Data were analyzed using one-way ANOVA and Tukey’s tests, as well as Kruskal–Wallis and Dunn’s tests, with a significance level of 5%. RHE showed compatible amounts of flavonoids and phenols, with an EC50 of 19.53 µg/mL. Through HPLC-DAD and GC-MS, biomolecules such as rosmarinic acid and α-Pinene were identified. The extract exhibited microbicidal activity and antibiofilm action, with reduction percentages of up to 69.6% (p < 0.05), showing superior performance compared to 0.12% chlorhexidine against C. albicans + A. baumannii. In conclusion, RHE may be a promising therapeutic agent against multidrug-resistant pathogens. Full article

(This article belongs to the Topic From Plant to Pharmacology: Understanding the Metabolism of Natural Products)

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20 pages, 979 KB

Open AccessArticle

Influence of Nutrient Medium Composition on the Redistribution of Valuable Metabolites in the Freshwater Green Alga Tetradesmus obliquus (Chlorophyta) Under Photoautotrophic Growth Conditions

by Elvira E. Ziganshina and Ayrat M. Ziganshin

BioTech 2025, 14(3), 60; https://doi.org/10.3390/biotech14030060 - 11 Aug 2025

Cited by 1

Abstract

The study of microalgae has led to significant progress in recent decades. The current microalgal biomass yield is unsatisfactory, except for certain species that are cultivated for the nutraceutical and pharmaceutical industries. In this study, the growth efficiency and biochemical composition of Tetradesmus [...] Read more.

The study of microalgae has led to significant progress in recent decades. The current microalgal biomass yield is unsatisfactory, except for certain species that are cultivated for the nutraceutical and pharmaceutical industries. In this study, the growth efficiency and biochemical composition of Tetradesmus obliquus at high levels of nutrients were characterized. Increasing the NH₄⁺-N content in the medium to 164 mg L⁻¹ allowed the algae to steadily accumulate biomass (6.14 ± 0.28 g L⁻¹) with a moderate content of starch. Optimizing the levels of N, P, and S allowed the biomass productivity to increase from the average 0.45 to 0.88 g L⁻¹ day⁻¹. A further increase of NH₄⁺-N to 410 mg L⁻¹ and other nutrients’ concentration allowed the algae to accumulate biomass (7.50 ± 0.28 g L⁻¹), enriched with protein and pigments. The algae cultivated with the high load of nutrients reached 100%, 84%, and 96% removal of N, P, and S, respectively. Adding the NaHCO₃ to the photobioreactor for pH adjustment (instead of NaOH) did not significantly improve the growth parameters or affect the composition of the algal cells. In general, our study will improve the comprehensive understanding of culture-based approaches to study the perspective use of the alga T. obliquus. Full article

(This article belongs to the Special Issue A Sustainable Approach to Macroalgae and Microalgae: From Cultivation to Compound Recovery and Biotechnological Applications)

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12 pages, 505 KB

Open AccessArticle

Effect of Ultrasonic Pretreatment on the Extraction Process of Essential Oils from Grapefruit (Citrus paradisi) By-Products

by Francisco Cadena-Cadena, Joe Luis Arias-Moscoso, Leandris Argentel-Martínez, Jony R. Torres Velazquez, Dulce Alondra Cuevas-Acuña, Nydia Estrellita Buitimea Cantua and Bartolo Concha-Frías

BioTech 2025, 14(3), 59; https://doi.org/10.3390/biotech14030059 - 7 Aug 2025

Abstract

This study evaluated the effect of ultrasonic pulse-assisted extraction on the yield and antioxidant activity of essential oils from grapefruit (Citrus paradisi) by-products using hydrodistillation and Soxhlet solvent extraction (hexane, acetone, ethanol). Ultrasound was applied at 40% amplitude for 20 min [...] Read more.

This study evaluated the effect of ultrasonic pulse-assisted extraction on the yield and antioxidant activity of essential oils from grapefruit (Citrus paradisi) by-products using hydrodistillation and Soxhlet solvent extraction (hexane, acetone, ethanol). Ultrasound was applied at 40% amplitude for 20 min before extraction. Results showed that ultrasound significantly increased extraction yield with hexane (from 2.6 ± 0.58% to 7.6 ± 1.5%) and acetone (from 8.6 ± 0.96% to 12 ± 1.4%), while ultrasound-assisted hydrodistillation nearly doubled the yield (from 0.7 ± 0.03% to 1.5 ± 0.49%). In contrast, ultrasound decreased yield with ethanol by 3%. Antioxidant activity measured by TEAC assay was highest in acetone extracts without ultrasound (13,366.5 ± 7.66 mmol TE/g) and ethanol extracts (12,606.8 ± 0.51 mmol TE/g). However, ultrasound combined with ethanol increased DPPH scavenging activity from 1073.5 ± 1.07 µg/mL to 4933.3 ± 0.71 µg/mL and maintained high flavonoid content (9.41 ± 0.15 mg/mL) and phenolics (5.33 ± 0.09 mg/mL). Ultrasound-assisted hydrodistillation also enhanced antioxidant capacity, with DPPH values rising from 51.82 ± 5.56 µg/mL to 2413.03 ± 3.17 µg/mL. These findings demonstrate that ultrasound effectively enhances essential oil extraction and antioxidant activity depending on the solvent used, underscoring the potential of this clean technology for valorizing citrus by-products. Full article

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21 pages, 763 KB

Open AccessReview

Pathway Analysis Interpretation in the Multi-Omic Era

by William G. Ryan V., Smita Sahay, John Vergis, Corey Weistuch, Jarek Meller and Robert E. McCullumsmith

BioTech 2025, 14(3), 58; https://doi.org/10.3390/biotech14030058 - 29 Jul 2025

Abstract

In bioinformatics, pathway analyses are used to interpret biological data by mapping measured molecules with known pathways to discover their functional processes and relationships. Pathway analysis has become an essential tool for interpreting large-scale omics data, translating complex gene sets into actionable experimental [...] Read more.

In bioinformatics, pathway analyses are used to interpret biological data by mapping measured molecules with known pathways to discover their functional processes and relationships. Pathway analysis has become an essential tool for interpreting large-scale omics data, translating complex gene sets into actionable experimental insights. However, issues inherent to pathway databases and misinterpretations of pathway relevance often result in “pathway fails,” where findings, though statistically significant, lack biological applicability. For example, the Tumor Necrosis Factor (TNF) pathway was originally annotated based on its association with observed tumor necrosis, while it is multifunctional across diverse physiological processes in the body. This review broadly evaluates pathway analysis interpretation, including embedding-based, semantic similarity-based, and network-based approaches to clarify their ideal use-case scenarios. Each method for interpretation is assessed for its strengths, such as high-quality visualizations and ease of use, as well as its limitations, including data redundancy and database compatibility challenges. Despite advancements in the field, the principle of “garbage in, garbage out” (GIGO) shows that input quality and method choice are critical for reliable and biologically meaningful results. Methodological standardization, scalability improvements, and integration with diverse data sources remain areas for further development. By providing critical guidance with contextual examples such as TNF, we aim to help researchers align their objectives with the appropriate method. Advancing pathway analysis interpretation will further enhance the utility of pathway analysis, ultimately propelling progress in systems biology and personalized medicine. Full article

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

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23 pages, 2175 KB

Open AccessArticle

Fetal Health Diagnosis Based on Adaptive Dynamic Weighting with Main-Auxiliary Correction Network

by Haiyan Wang, Yanxing Yin, Liu Wang, Yifan Wang, Xiaotong Liu and Lijuan Shi

BioTech 2025, 14(3), 57; https://doi.org/10.3390/biotech14030057 - 28 Jul 2025

Abstract

Maternal and child health during pregnancy is an important issue in global public health, and the classification accuracy of fetal cardiotocography (CTG), as a key tool for monitoring fetal health during pregnancy, is directly related to the effectiveness of early diagnosis and intervention. [...] Read more.

Maternal and child health during pregnancy is an important issue in global public health, and the classification accuracy of fetal cardiotocography (CTG), as a key tool for monitoring fetal health during pregnancy, is directly related to the effectiveness of early diagnosis and intervention. Due to the serious category imbalance problem of CTG data, traditional models find it challenging to take into account a small number of categories of samples, increasing the risk of leakage and misdiagnosis. To solve this problem, this paper proposes a two-step innovation: firstly, we design a method of adaptive adjustment of misclassification loss function weights (MAAL), which dynamically identifies and increases the focus on misclassified samples based on misclassification rates. Secondly, a primary and secondary correction network model (MAC-NET) is constructed to carry out secondary correction for the misclassified samples of the primary model. Experimental results show that the method proposed in this paper achieves 99.39% accuracy on the UCI publicly available fetal health dataset, and also obtains excellent performance on other domain imbalance datasets. This demonstrates that the model is not only effective in alleviating the problem of category imbalance, but also has very high clinical utility. Full article

(This article belongs to the Section Computational Biology)

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16 pages, 982 KB

Open AccessArticle

Impact of Cattle Breed in scRNA-Seq Reference on Muscle Fiber Type Deconvolution from Bulk RNA-Seq: A Comparison of Software Tools

by Raphael P. Moreira, Marcelo R. Vicari, Henrique A. Mulim, Theresa M. Casey, Jacquelyn Boerman, Xing Fu and Hinayah R. Oliveira

BioTech 2025, 14(3), 56; https://doi.org/10.3390/biotech14030056 - 25 Jul 2025

Abstract

While bulk RNA sequencing provides a comprehensive view of transcriptomes, it lacks cell type specificity. Single-cell RNA sequencing (scRNA-seq) overcomes this limitation by providing detailed insights at the individual cell level, though it involves higher costs. Deconvolution methods can estimate cell type proportions [...] Read more.

While bulk RNA sequencing provides a comprehensive view of transcriptomes, it lacks cell type specificity. Single-cell RNA sequencing (scRNA-seq) overcomes this limitation by providing detailed insights at the individual cell level, though it involves higher costs. Deconvolution methods can estimate cell type proportions in bulk RNA-seq data, but their results may vary based on the scRNA-seq reference data and software used. This study investigates the estimation of muscle fiber type proportions through deconvolution analysis of Longissimus dorsi muscle bulk RNA-seq data from late-gestation Holstein Friesian multiparous cows. Four software tools (i.e., CIBERSORTx, Cellanneal, DeconvR-NNLS, and DeconvR-RLM) were compared using scRNA-seq reference data from Brahman and Wagyu cattle breeds, which included proportions of types I, IIa, and IIx myofibers. Kruskal–Wallis and Dunn’s tests revealed that the breed of reference data significantly influenced the proportions of type IIa and IIx muscle fibers across different deconvolution methods. To the best of our knowledge, this is the first study to show that the cattle breed used in reference scRNA-seq data can substantially impact deconvolution outcomes, highlighting a critical consideration for accurate cell type proportion estimation in livestock genomics. These findings suggest that future deconvolution studies should carefully consider breed compatibility between reference and target datasets. Full article

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14 pages, 1901 KB

Open AccessArticle

The Role of Microarray in Modern Sequencing: Statistical Approach Matters in a Comparison Between Microarray and RNA-Seq

by Isaac D. Raplee, Samiksha A. Borkar, Li Yin, Guglielmo M. Venturi, Jerry Shen, Kai-Fen Chang, Upasana Nepal, John W. Sleasman and Maureen M. Goodenow

BioTech 2025, 14(3), 55; https://doi.org/10.3390/biotech14030055 - 5 Jul 2025

Cited by 1

Abstract

Gene expression analysis is crucial in understanding cellular processes, development, health, and disease. With RNA-seq outpacing microarray as the chosen platform for gene expression, is there space for array data in future profiling? This study involved 35 participants from the Adolescent Medicine Trials [...] Read more.

Gene expression analysis is crucial in understanding cellular processes, development, health, and disease. With RNA-seq outpacing microarray as the chosen platform for gene expression, is there space for array data in future profiling? This study involved 35 participants from the Adolescent Medicine Trials Network for HIV/AIDS Intervention protocol. RNA was isolated from whole blood samples and analyzed using both microarray and RNA-seq technologies. Data processing included quality control, normalization, and statistical analysis using non-parametric Mann–Whitney U tests. Differential expression analysis and pathway analysis were conducted to compare the outputs of the two platforms. The study found a high correlation in gene expression profiles between microarray and RNA-seq, with a median Pearson correlation coefficient of 0.76. RNA-seq identified 2395 differentially expressed genes (DEGs), while microarray identified 427 DEGs, with 223 DEGs shared between the two platforms. Pathway analysis revealed 205 perturbed pathways by RNA-seq and 47 by microarray, with 30 pathways shared. Both microarray and RNA-seq technologies provide highly concordant results when analyzed with consistent non-parametric statistical methods. The findings emphasize that both methods are reliable for gene expression analysis and can be used complementarily to enhance the robustness of biological insights. Full article

(This article belongs to the Section Computational Biology)

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