Journal Description
Applied Biosciences
Applied Biosciences
is an international, peer-reviewed, open access journal on all aspects of applied biosciences published quarterly online by MDPI.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within ESCI (Web of Science), Scopus and other databases.
- Journal Rank: CiteScore - Q2 (Immunology and Microbiology (miscellaneous))
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 19.1 days after submission; acceptance to publication is undertaken in 5.3 days (median values for papers published in this journal in the second half of 2024).
- Recognition of Reviewers: APC discount vouchers, optional signed peer review, and reviewer names published annually in the journal.
- Applied Biosciences is a companion journal of Applied Sciences.
Latest Articles
Linear DNA–Chitosan Nanoparticles: Formulation Challenges and Transfection Efficiency in Lung Cell Line
Appl. Biosci. 2025, 4(2), 29; https://doi.org/10.3390/applbiosci4020029 - 6 Jun 2025
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Linear DNA constructs are used in gene delivery and therapy application due to their capacity of integration into the mammalian genome, offering stable transgene expression. Compared to circular plasmids, linear DNA also has the advantage that its dimension and steric hindrance are directly
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Linear DNA constructs are used in gene delivery and therapy application due to their capacity of integration into the mammalian genome, offering stable transgene expression. Compared to circular plasmids, linear DNA also has the advantage that its dimension and steric hindrance are directly correlated to the length of the nucleotide chain. These considerations make linear DNA an effective choice for gene delivery pilot studies, where formulations and transfection efficiency calculations are studied considering the nucleic acid dimensions. Meanwhile, the development of DNA–chitosan nanoparticles (NPs) has gained significant interest for their potential in nucleic acid delivery, especially as non-viral gene delivery systems and for embedding linear DNA fragments, as well as gene delivery to the lung. This study explored an easy polyelectrolyte complexing preparation of linear DNA-loaded chitosan nanoparticles. Among the different formulations of nanoparticles prepared, the optimal one exhibited a size of approximately 290 nm, an encapsulation efficiency of 86% and a zeta potential of 25 mV. Additionally, this study examined how the concentration of DNA in solution influenced nanoparticle formation, encapsulation efficiency and particle size. In particular, transient transfection of the chitosan–linear DNA fragment complex, encoding for green fluorescent protein (GFP), was conducted in human pulmonary distal lung cells (NCI-H441 cells), demonstrating successful cellular internalization and protein expression. These studies highlight the potential of DNA–chitosan NPs in nucleic acid delivery, particularly for pulmonary applications. Future works will focus on formulating the achieved carrier into an inhalable dosage form to improve its translational application.
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Open AccessArticle
A Flow Cytometry Protocol for Measurement of Plant Genome Size Using Frozen Material
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Abhishek Soni, Lena Constantin, Agnelo Furtado and Robert J Henry
Appl. Biosci. 2025, 4(2), 28; https://doi.org/10.3390/applbiosci4020028 - 4 Jun 2025
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Flow cytometry is widely applied to infer the ploidy and genome size (GS) of plant nuclei. The conventional approach of sample preparation, reliant on fresh plant material to release intact nuclei, often results in poor yields of nuclei in conditions when a plant
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Flow cytometry is widely applied to infer the ploidy and genome size (GS) of plant nuclei. The conventional approach of sample preparation, reliant on fresh plant material to release intact nuclei, often results in poor yields of nuclei in conditions when a plant material cannot be kept fresh due to logistical constraints. Previous attempts to use frozen plant material were mainly limited to ploidy analysis and relied on chopping methods, which restrict the material input and often result in poor nuclei yield, especially in frozen samples, due to incomplete disruption. Here, we present a modified protocol for GS estimation using frozen plant material that facilitates larger volumes of tissue to be processed while improving debris removal. Nuclei isolated from this protocol can also be used for DNA or RNA extraction. Genome size estimates from frozen material are similar to those from fresh material, with a reduction in error range, although not always significant (p > 0.05). In certain species, frozen samples can yield substantially more nuclei than fresh material. With the addition of specific debris compensation algorithms, coefficient of variation (CV%) can be maintained below 5%. This method has special value in estimating the GS of samples collected from remote locations and frozen for use in plant genome sequencing. Freezing preserves high-quality DNA and RNA, enabling the same sample to be used for both flow cytometry and genome sequencing.
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Open AccessArticle
Green Synthesis and Characterization of Iron Oxide Nanoparticles Using Egeria densa Plant Extract
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Maruf Olaide Yekeen, Mubarak Ibrahim, James Wachira and Saroj Pramanik
Appl. Biosci. 2025, 4(2), 27; https://doi.org/10.3390/applbiosci4020027 - 2 Jun 2025
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An aqueous leaf extract of Egeria densa was used to green-synthesize iron (II) and iron (III) oxide nanoparticles from ferrous sulphate and ferric chloride, respectively. The successful green synthesis of the nanoparticles was confirmed through UV–visible spectroscopy, and the colour of the mixtures
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An aqueous leaf extract of Egeria densa was used to green-synthesize iron (II) and iron (III) oxide nanoparticles from ferrous sulphate and ferric chloride, respectively. The successful green synthesis of the nanoparticles was confirmed through UV–visible spectroscopy, and the colour of the mixtures changed from light-yellow to green-black and reddish-brown for FeO–NPs and Fe2O3–NPs, respectively. The morphological characteristics of the nanoparticles were determined using an X-ray diffractometer (XRD), a Fourier transform infrared spectrophotometer (FTIR), a transmission electron microscope (TEM), and energy-dispersive X-ray spectroscopy (EDX). The UV–Vis spectrum of the FeO–NPs showed a sharp peak at 290 nm due to the surface plasmon resonance, while that of the Fe2O3–NPs showed a sharp peak at 300 nm. TEM analysis revealed that the FeO–NPs were oval to hexagonal in shape and were clustered together with an average size of 18.49 nm, while the Fe2O3-NPs were also oval to hexagonal in shape, but some were irregularly shaped, and they clustered together with an average size of 27.96 nm. EDX analysis showed the presence of elemental iron and oxygen in both types of nanoparticles, indicating that these nanoparticles were essentially present in oxide form. The XRD patterns of both the FeO–NPs and Fe2O3–NPs depicted that the nanoparticles produced were crystalline in nature and exhibited the rhombohedral crystal structure of hematite. The FT-IR spectra revealed that phenolic compounds were present on the surface of the nanoparticles and were responsible for reducing the iron salts into FeO–NPs and Fe2O3–NPs. Conclusively, this work demonstrated for the first time the ability of Elodea aqueous extract to synthesize iron-based nanoparticles from both iron (II) and iron (III) salts, highlighting its versatility as a green reducing and stabilizing agent. The dual-path synthesis approach provides new insights into the influence of the precursor oxidation state on nanoparticle formation, thereby expanding our understanding of plant-mediated nanoparticle production and offering a sustainable route for the fabrication of diverse iron oxide nanostructures. Furthermore, it provides a simple, cost-effective, and environmentally friendly method for the synthesis of the FeO–NPs and Fe2O3–NPs using Egeria densa.
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Open AccessReview
Edible Terrestrial Cyanobacteria for Food Security in the Context of Climate Change: A Comprehensive Review
by
Midori Kurahashi and Angelica Naka
Appl. Biosci. 2025, 4(2), 26; https://doi.org/10.3390/applbiosci4020026 - 16 May 2025
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This review examines the history of consumption, life cycle, and culture conditions of seven edible mucilaginous terrestrial cyanobacterial strains—Nostoc flagelliforme, Nostoc commune, Nostoc sphaeroides, Nostoc sphaericum, Nostoc verrucosum, Aphanothece sacrum, and Nostochopsis lobatus—as resilient and
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This review examines the history of consumption, life cycle, and culture conditions of seven edible mucilaginous terrestrial cyanobacterial strains—Nostoc flagelliforme, Nostoc commune, Nostoc sphaeroides, Nostoc sphaericum, Nostoc verrucosum, Aphanothece sacrum, and Nostochopsis lobatus—as resilient and sustainable food sources in the face of climate change. Traditionally consumed across various cultures and known for their resilience in extreme environments, these cyanobacteria offer high nutritional value, including proteins, vitamins, and essential fatty acids, making them promising candidates for addressing food security. Their ability to fix nitrogen reduces reliance on synthetic fertilizers, enhancing agricultural applications by improving soil fertility and minimizing dependence on fossil fuel-derived chemicals. Unlike conventional crops, these cyanobacteria require minimal resources and do not compete for arable land, positioning them as ideal candidates for low-impact food production. Despite these advantages, the review highlights the need for scalable and cost-effective cultivation methods to fully realize their potential in supporting a resilient global food supply. Additionally, it underscores the importance of ensuring their safety for consumption, particularly regarding toxin content.
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Open AccessArticle
Direct Expression of CPT1a Enables a High Throughput Platform for the Discovery of CPT1a Modulators
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Jason Chen, Tuyen Tran, Anthony Wong, Luofei Wang, Pranavi Annaluru, Vibha Sreekanth, Samika Murthy, Laasya Munjeti, Tanya Park, Utkarsh Bhat, Glynnis Leong, Yumeng Li, Simeng Chen, Natalie Kong, Rushika Raval, Yining Xie, Shreya Somani, Aditi Manohar Bhambhani, Zoey Zhu, Landen Chu, Kimai Dosch, Edward Njoo and Zhan Chenadd
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Appl. Biosci. 2025, 4(2), 25; https://doi.org/10.3390/applbiosci4020025 - 12 May 2025
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Carnitine palmitoyltransferase 1 (CPT1), which catalyzes the rate-limiting step of fatty acid oxidation, has been implicated in therapeutic approaches to several human diseases characterized by aberrant lipid metabolism. The isoform-specific quantification of CPT1 activity is essential in the characterization of small molecule inhibitors
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Carnitine palmitoyltransferase 1 (CPT1), which catalyzes the rate-limiting step of fatty acid oxidation, has been implicated in therapeutic approaches to several human diseases characterized by aberrant lipid metabolism. The isoform-specific quantification of CPT1 activity is essential in the characterization of small molecule inhibitors of CPT1, but several existing means to quantify enzymatic activity, including the use of radioisotope-labeled carnitine, are not amenable to scalable, high throughput screening. Here, we demonstrate that mitochondrial extracts from Expi293 cells transfected with a CPT1a plasmid are a reliable and robust source of catalytically active human CPT1. Moreover, with a source of catalytically active enzyme in hand, we modified a previously reported colorimetric method of coenzyme A (CoA) easily scalable to a 96-well format for the screening of CPT1a inhibitors. This assay platform was validated by two previously reported inhibitors of CPT1a: R-etomoxir and perhexiline. To further demonstrate the applicability of this method in small molecule screening, we prepared and screened a library of 87 known small molecule APIs, validating the inhibitory effect of chlorpromazine on CPT1.
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Open AccessReview
Urinary Markers for Prostate Cancer: State of the Art
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Carlo Giorgio Costi, Serena Sartori, Riccardo Danuso, Andrea Piasentin, Paolo Umari and Giovanni Liguori
Appl. Biosci. 2025, 4(2), 24; https://doi.org/10.3390/applbiosci4020024 - 8 May 2025
Abstract
Prostate cancer (PCa) is one of the most common malignancies in men, where early and accurate detection is crucial. While PSA testing has been the diagnostic standard, its limited specificity leads to unnecessary biopsies and missed significant cancers. Urinary biomarkers such as PCA3
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Prostate cancer (PCa) is one of the most common malignancies in men, where early and accurate detection is crucial. While PSA testing has been the diagnostic standard, its limited specificity leads to unnecessary biopsies and missed significant cancers. Urinary biomarkers such as PCA3 and TMPRSS2-ERG and multi-marker assays (MyProstateScore, SelectMDx, and ExoDx) offer a promising alternative. This narrative review examines their diagnostic performance and clinical utility with the aim of understanding whether they can be integrated with the established tests and exams already in use. A literature search of PubMed, Scopus, and Medline identified some relevant recent studies (2010–2025). The findings show that PCA3 and TMPRSS2-ERG improve specificity over PSA, while multi-marker tests enhance risk stratification and reduce unnecessary procedures. MPS integrates urinary biomarkers with PSA, achieving over 95% sensitivity and negative predictive value for clinically significant cancers. SelectMDx demonstrates ~90% negative predictive value, and ExoDx assesses urinary exosomes to predict aggressive disease. Despite their advantages, challenges persist, including variability in performance, cost, and accessibility. Urinary biomarkers represent a major step toward more precise, less invasive diagnostics, with future research needed to optimize clinical integration and cost-effectiveness.
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(This article belongs to the Special Issue Feature Review for Applied Biosciences)
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Open AccessReview
Can Caenorhabditis elegans Serve as a Reliable Model for Drug and Nutraceutical Discovery?
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Opeyemi. O. Deji-Oloruntoba, Taiwo. O. Elufioye, Stephen Adeniyi Adefegha and Miran Jang
Appl. Biosci. 2025, 4(2), 23; https://doi.org/10.3390/applbiosci4020023 - 2 May 2025
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Experimental research demands the selection of appropriate models to align with study objectives and conditions. Traditional experimental models, such as in vivo animal studies and in vitro systems like organoids, present nutraceutical and pharmaceutical research limitations such as high cost, ethical concerns, long
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Experimental research demands the selection of appropriate models to align with study objectives and conditions. Traditional experimental models, such as in vivo animal studies and in vitro systems like organoids, present nutraceutical and pharmaceutical research limitations such as high cost, ethical concerns, long lifespan, and difficult genetic manipulation. Caenorhabditis elegans has proved to be a valuable model as a result of its genetic and physiological similarities to higher organisms, fully sequenced genome, short life cycle, and transparency. These features enable high-throughput screening, molecular pathway analysis, and lifespan and healthspan assays. C. elegans has significantly advanced the discovery of bioactive molecules with therapeutic potential, shedding light on aging, neurodegeneration, metabolic disorders, and immune responses. Its utility in pharmacokinetics and validation of nutraceuticals underscores its role in longevity and metabolic health research. Additionally, its conserved stress response, apoptosis, and pathogen recognition pathways facilitate the study of pharmacological interventions for inflammation, oxidative stress, and infections. This study evaluates the applicability of C. elegans as a model for in vivo screening, analyses its role in drug efficacy testing, and discusses relevant advancements, associated difficulties, and what to expect of C. elegans in research.
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Open AccessArticle
Maximizing Common Bean (Phaseolus vulgaris L.) Productivity Through Application of Organic and Inorganic Fertilizers in Alkaline Soil
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Safiullah Habibi, Shafiqullah Aryan, Ali Yawar Seerat, Kalimullah Saighani and Mohammad Daud Haidari
Appl. Biosci. 2025, 4(2), 22; https://doi.org/10.3390/applbiosci4020022 - 1 May 2025
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Common beans are a vital source of protein, vitamins, and minerals. Increasing common beans productivity is crucial for improving food security and farmers’ incomes globally. This study evaluated the growth and yield responses of common beans to integrated organic and inorganic fertilizers under
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Common beans are a vital source of protein, vitamins, and minerals. Increasing common beans productivity is crucial for improving food security and farmers’ incomes globally. This study evaluated the growth and yield responses of common beans to integrated organic and inorganic fertilizers under field conditions at the Faculty of Agriculture, Kabul University. The trial was repeated over two consecutive growing seasons in 2020 and 2021, using a randomized complete block design with 18 treatments and three replications. The fertilizers used included urea (N) (0, 60, and 90 kg/ha), diammonium phosphate (D) (0, 50, and 100 kg/ha), and farmyard manure (O) (0 and 5000 kg/ha). The results show that integrated fertilizers, particularly O5000N60D50, O5000N60D100, O5000N90D50, and O5000N90D100, significantly increased growth and yield parameters. In 2020, the grain yield increased significantly (p < 0.05) by 75.6, 76.7, and 68.4% with the O5000N60D50, O5000N60D100, and O5000N90D100 treatments, respectively. In 2021, O5000N60D50, O5000N60D100, and O5000N90D50 showed significant yield increases of 94.7, 89.6, and 97.9%, respectively. The grain yield strongly correlated with the SPAD value (r = 0.84), number of pods per plant (r = 0.71), and number of seeds per pod (r = 0.66) in 2020, and it more strongly correlated with the SPAD value (r = 0.91), number of pods per plant (r = 0.77), and number of seeds per pod (r = 0.76) in 2021. A principal component analysis highlighted the effectiveness of organic–inorganic fertilizer combinations, particularly O5000N60D50, in enhancing productivity while potentially reducing inorganic fertilizer application. This study demonstrates that integrating organic and inorganic fertilizers enhances sustainable crop productivity and reduces negative environmental impacts, particularly in regions facing nutrient depletion and drought conditions.
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Open AccessCommunication
Bioactive Factors Isolated and Purified from Bovine Colostrum Can Restore Extracellular Matrix Under Degradation by Metalloproteinases
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Federica Coppa, Graziella Giuffrida, Giulia Iannello, Stefania Pennisi, Greta Ferruggia and Maria Violetta Brundo
Appl. Biosci. 2025, 4(2), 21; https://doi.org/10.3390/applbiosci4020021 - 8 Apr 2025
Abstract
The ECM is composed of a considerable number of biochemically and structurally diverse constituents. ECM is a highly dynamic system that constantly receives and sends biological, chemical and mechanical signals. Several studies suggest that mechanical signals derived from the extracellular microenvironment regulate skin
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The ECM is composed of a considerable number of biochemically and structurally diverse constituents. ECM is a highly dynamic system that constantly receives and sends biological, chemical and mechanical signals. Several studies suggest that mechanical signals derived from the extracellular microenvironment regulate skin regeneration and wound healing. Tests measuring collagen contraction showed a significant difference in contraction activation in samples treated with the 2% colostrum derivative mixture compared to the control. The analysis of the supernatant showed an inhibition of metalloproteinase-2 expression and an increase in collagen secretion by fibroblasts in treatment samples. Our hypothesis is that the molecules extracted and purified from bovine colostrum can restore the ECM environment qualitative and quantitative characteristics, thus permitting, through a mechanical action, the restoration of the wound due to the transduction of the signal activated by the integrins.
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(This article belongs to the Special Issue Anatomy and Regenerative Medicine: From Methods to Applications)
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Open AccessArticle
Umckalin Promotes Melanogenesis in B16F10 Cells Through the Activation of Wnt/β-Catenin and MAPK Signaling Pathways
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So-Yeon Oh and Chang-Gu Hyun
Appl. Biosci. 2025, 4(2), 20; https://doi.org/10.3390/applbiosci4020020 - 2 Apr 2025
Abstract
Melanogenesis is regulated by melanogenic enzymes such as tyrosinase (TYR), TRP-1, and TRP-2, whose expression is controlled by the microphthalmia-associated transcription factor (MITF). Various signaling pathways, including cAMP/PKA, MAPK/ERK, Wnt/β-catenin, and PI3K/Akt, are involved in this process and have been a focal point
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Melanogenesis is regulated by melanogenic enzymes such as tyrosinase (TYR), TRP-1, and TRP-2, whose expression is controlled by the microphthalmia-associated transcription factor (MITF). Various signaling pathways, including cAMP/PKA, MAPK/ERK, Wnt/β-catenin, and PI3K/Akt, are involved in this process and have been a focal point of research for treating pigmentation disorders. However, developing effective therapies for conditions like vitiligo remains a significant challenge. In this study, the effects of umckalin on melanogenesis and its molecular mechanisms were investigated using B16F10 cells, a mouse melanoma cell line widely used as a model for melanin production studies. B16F10 cells produce melanin via melanosomes and express key melanogenic enzymes such as TYR, TRP-1, and TRP-2, making them a reliable model system. Our findings demonstrate that umckalin promotes melanogenesis in a concentration-dependent manner by upregulating TRP-1 expression and activating the MITF signaling pathway. Additionally, umckalin modulated key signaling pathways, including GSK3β/β-catenin and MAPK, to enhance melanogenesis. In conclusion, umckalin enhances melanogenic enzyme activity by activating critical signaling pathways, thereby promoting melanin synthesis. These findings suggest that umckalin could be a promising candidate for developing therapeutic agents for pigmentation disorders such as vitiligo. Further studies are required to explore its mechanisms and clinical applications in greater detail.
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(This article belongs to the Special Issue Plant Natural Compounds: From Discovery to Application)
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Open AccessReview
Enzymatic Oxidants, Antioxidants, and Inflammatory Bowel Disease
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R. Steven Esworthy
Appl. Biosci. 2025, 4(2), 19; https://doi.org/10.3390/applbiosci4020019 - 1 Apr 2025
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The role of oxidants and antioxidants in inflammatory bowel disease (IBD) has been actively explored since the early 1980s, starting with the role of the respiratory burst of neutrophils and ischemia in bowel pathology. Since that time, the enzymatic components contributing to the
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The role of oxidants and antioxidants in inflammatory bowel disease (IBD) has been actively explored since the early 1980s, starting with the role of the respiratory burst of neutrophils and ischemia in bowel pathology. Since that time, the enzymatic components contributing to the pool of reactive oxygen species, including superoxide, H2O2, and lipid hydroperoxides, and the counteracting antioxidants—catalase, glutathione peroxidases (Gpx), peroxiredoxins (PRDX), superoxide dismutases, and others—have been fleshed out. My perspective on IBD is from the role of the balance or imbalance of enzymatic oxidant sources and enzymatic antioxidants in the inflammatory process. I will present evidence on the involvement of oxidant and antioxidant processes in IBD based, as much as possible, on my experiences with Gpxs. This evidence will be discussed in terms of both the immune system and local bowel oxidant and antioxidant systems. As Gpxs are generally selenium-dependent, possible deficiencies in selenium uptake in active IBD and the impact on Gpx expression will be explored. The more recently introduced ferroptosis, an iron-dependent lipid peroxidation-based pathological process, will be reviewed for its possible involvement in IBD.
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(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2024)
Open AccessArticle
AssayBLAST: A Bioinformatic Tool for In Silico Analysis of Molecular Multiparameter Assays
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Maximilian Collatz, Sascha D. Braun, Martin Reinicke, Elke Müller, Stefan Monecke and Ralf Ehricht
Appl. Biosci. 2025, 4(2), 18; https://doi.org/10.3390/applbiosci4020018 - 1 Apr 2025
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Accurate primer and probe design is essential for molecular applications, including PCR, qPCR, and molecular multiparameter assays like microarrays. The novel software tool AssayBLAST addresses this need by simulating interactions between oligonucleotides and target sequences. AssayBLAST handles large sets of primer and probe
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Accurate primer and probe design is essential for molecular applications, including PCR, qPCR, and molecular multiparameter assays like microarrays. The novel software tool AssayBLAST addresses this need by simulating interactions between oligonucleotides and target sequences. AssayBLAST handles large sets of primer and probe sequences simultaneously and supports comprehensive assay designs by allowing users to identify off-target binding, calculate melting temperatures, and ensure strand specificity, a critical but often overlooked aspect. AssayBLAST performs two optimized BLAST-based searches for each primer or probe sequence, checking the forward and reverse strands for off-target interactions and strand-specific binding accuracy. The results are compiled into a mapping table containing binding sites, mismatches, and strand orientation, allowing users to validate large sets of oligonucleotides across predefined custom databases for a complete and optimal theoretical assay design. AssayBLAST was evaluated against experimental Staphylococcus aureus microarray data, achieving 97.5% accuracy in predicting probe–target hybridization outcomes. This high accuracy demonstrates the method’s effectiveness in reliably using BLAST hits and mismatch counts to predict microarray results. AssayBLAST provides a reliable, scalable solution for in silico primer and probe validation, effectively supporting large-scale assay designs and optimizations. Its accurate prediction of hybridization outcomes demonstrates its utility in enhancing the efficiency and reliability of molecular assays.
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Open AccessReview
Bacterial Sialidases: Biological Significance and Application
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Stephan Engibarov, Yana Gocheva, Irina Lazarkevich and Rumyana Eneva
Appl. Biosci. 2025, 4(2), 17; https://doi.org/10.3390/applbiosci4020017 - 1 Apr 2025
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This review summarizes recent findings on the diverse roles of bacterial sialidases in microbial biology. Bacterial sialidases, also known as neuraminidases, are exog α-lycosidases that cleave terminal sialic acid residues from a number of complex compounds designated as sialoglycoconjugates (glycoproteins, glycolipids and oligosaccharides).
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This review summarizes recent findings on the diverse roles of bacterial sialidases in microbial biology. Bacterial sialidases, also known as neuraminidases, are exog α-lycosidases that cleave terminal sialic acid residues from a number of complex compounds designated as sialoglycoconjugates (glycoproteins, glycolipids and oligosaccharides). Metabolically, they are involved in sialic acid catabolism, providing energy, carbon and nitrogen sources. Catabolic degradation of sialic acids is a physiological feature that can be considered an important virulence factor in pathogenic microorganisms. Sialidases play a pivotal role in host–pathogen interactions and promotion of bacterial colonization. The activity of these enzymes enables bacterial adhesion, biofilm formation, tissue invasion, and also provides immune evasion by exposing cryptic receptors and modifying immune components. Many different perspectives are being developed for the potential application of sialidases. In the field of medicine, they are being explored as appropriate targets for antimicrobials, vaccines, diagnostic preparations and in tumor immunotherapy. In the field of enzymatic synthesis, they are used for the regioselective production of oligosaccharide analogs, enzymatic separation of isoenzymes and as a tool for structural analysis of sialylated glycans, among other applications.
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Open AccessReview
Advancements in Nanotechnology for Targeted and Controlled Drug Delivery in Hematologic Malignancies: Shaping the Future of Targeted Therapeutics
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Abdurraouf Mokhtar Mahmoud and Clara Deambrogi
Appl. Biosci. 2025, 4(1), 16; https://doi.org/10.3390/applbiosci4010016 - 5 Mar 2025
Cited by 1
Abstract
Hematologic malignancies, including leukemia, lymphoma, and multiple myeloma, pose significant therapeutic challenges due to their heterogeneity and high relapse rates. Nanotechnology has emerged as a promising avenue for precision drug delivery in these malignancies, allowing for enhanced drug concentration at tumor sites and
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Hematologic malignancies, including leukemia, lymphoma, and multiple myeloma, pose significant therapeutic challenges due to their heterogeneity and high relapse rates. Nanotechnology has emerged as a promising avenue for precision drug delivery in these malignancies, allowing for enhanced drug concentration at tumor sites and reducing systemic toxicity. Recent developments in nanocarriers—such as liposomes, polymeric nanoparticles, and inorganic nanoparticles—have enabled targeted approaches, utilizing molecular markers specific to malignant cells to increase therapeutic efficacy while minimizing adverse effects. Evidence from preclinical and clinical studies underscores the potential of nanotechnology to improve patient outcomes by facilitating controlled release, improved bioavailability, and reduced toxicity. However, translating these advancements into clinical practice requires further research to validate their safety and efficacy. This review provides a comprehensive analysis of the latest innovations in nanotechnology for targeted drug delivery in hematologic malignancies, addressing current achievements and future directions for integrating these approaches into Clinical Hemato-Oncology.
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(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2024)
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Open AccessArticle
Enhanced Protein Digestibility and Amino Acid Profile of a Novel Legume (Inga paterno) Seed Flours: Evaluation of Proximal Composition Changes by Sprouting
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Lizbeth Rosas-Ordoñez, Milena M. Ramírez-Rodrigues, Melissa A. Ramírez-Rodrigues and Taisa S. S. Pereira
Appl. Biosci. 2025, 4(1), 15; https://doi.org/10.3390/applbiosci4010015 - 5 Mar 2025
Abstract
The nutritional value of Inga paterno seeds remains largely unexplored. Given the global protein deficiency, underutilized legumes like I. paterno could serve as alternative protein sources. This study evaluated the effect of sprouting on the composition, protein digestibility (PD) as soluble protein (SP),
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The nutritional value of Inga paterno seeds remains largely unexplored. Given the global protein deficiency, underutilized legumes like I. paterno could serve as alternative protein sources. This study evaluated the effect of sprouting on the composition, protein digestibility (PD) as soluble protein (SP), amino acid profile, free amino acids by UHPLC, and nutritional indicators of I. paterno seed flour. Seeds were sprouted for 0, 2, 4, 6, 8, or 10 days, then dried, milled, and analyzed. The seeds reached 100% sprouting after six days. Sprouting led to a 54.36% decrease in protein content but a 109% increase in the lipid fraction by day six. PD doubled after 8–10 days of sprouting. Additionally, total amino acid content significantly increased and the chemical score of majority essential amino acids tripled. After in vitro digestion, sprouted flour released higher amounts of free amino acids, particularly aspartic acid (from 9.10 ± 0.18 to 19.65 ± 0.97 mg/L), histidine (from 33.48 ± 0.61 to 46.29 ± 2.34 mg/L), alanine (from 16.32 ± 0.40 to 23.74 ± 0.07 mg/L), and lysine (from no detected to 7.12 ± 0.36 m/L). These findings suggest that sprouted I. paterno seeds could be a valuable, digestible protein source with enhanced nutritional quality, making them a promising ingredient for the food industry.
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(This article belongs to the Special Issue Plant Natural Compounds: From Discovery to Application)
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Dynamic Patch-Based Sample Generation for Pulmonary Nodule Segmentation in Low-Dose CT Scans Using 3D Residual Networks for Lung Cancer Screening
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Ioannis D. Marinakis, Konstantinos Karampidis, Giorgos Papadourakis and Mostefa Kara
Appl. Biosci. 2025, 4(1), 14; https://doi.org/10.3390/applbiosci4010014 - 5 Mar 2025
Abstract
Lung cancer is by far the leading cause of cancer death among both men and women, making up almost 25% of all cancer deaths Each year, more people die of lung cancer than colon, breast, and prostate cancer combined. The early detection of
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Lung cancer is by far the leading cause of cancer death among both men and women, making up almost 25% of all cancer deaths Each year, more people die of lung cancer than colon, breast, and prostate cancer combined. The early detection of lung cancer is critical for improving patient outcomes, and automation through advanced image analysis techniques can significantly assist radiologists. This paper presents the development and evaluation of a computer-aided diagnostic system for lung cancer screening, focusing on pulmonary nodule segmentation in low-dose CT images, by employing HighRes3DNet. HighRes3DNet is a specialized 3D convolutional neural network (CNN) architecture based on ResNet principles which uses residual connections to efficiently learn complex spatial features from 3D volumetric data. To address the challenges of processing large CT volumes, an efficient patch-based extraction pipeline was developed. This method dynamically extracts 3D patches during training with a probabilistic approach, prioritizing patches likely to contain nodules while maintaining diversity. Data augmentation techniques, including random flips, affine transformations, elastic deformations, and swaps, were applied in the 3D space to enhance the robustness of the training process and mitigate overfitting. Using a public low-dose CT dataset, this approach achieved a Dice coefficient of 82.65% on the testing set for 3D nodule segmentation, demonstrating precise and reliable predictions. The findings highlight the potential of this system to enhance efficiency and accuracy in lung cancer screening, providing a valuable tool to support radiologists in clinical decision-making.
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(This article belongs to the Special Issue Neural Networks and Deep Learning for Biosciences)
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Phytochemical Profile, Antioxidant and Antimicrobial Activity of Two Species of Oak: Quercus sartorii and Quercus rysophylla
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Elizabeth Coyotl-Martinez, Juan Alex Hernández-Rivera, José L. Arturo Parra-Suarez, Sandra Raquel Reyes-Carmona and Alan Carrasco-Carballo
Appl. Biosci. 2025, 4(1), 13; https://doi.org/10.3390/applbiosci4010013 - 4 Mar 2025
Abstract
The genus Quercus (Fagaceae) is one of the most widely distributed and species-diverse trees in the Northern Hemisphere. The present study addresses the investigation of the phyto-chemical profile by ten assays, the antioxidant activity scavenging of DPPH radicals, total phenolic content, total flavonoids,
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The genus Quercus (Fagaceae) is one of the most widely distributed and species-diverse trees in the Northern Hemisphere. The present study addresses the investigation of the phyto-chemical profile by ten assays, the antioxidant activity scavenging of DPPH radicals, total phenolic content, total flavonoids, and antimicrobial activity against three pathogenic bacteria with the foliage of two species of red oak (Quercus sartorii and Quercus rysophylla). Both species of oak showed a high phenolic content in the aqueous extract (22,342.10 ± 3076.5 mg GAE/kg of plant and 17,747.14 ± 1139.9 mg GAE/kg of plant, respectively). In the flavonoid content, Q. sartorii showed a higher amount in the ethanolic extract (24,587.42 ± 996.3 mg QE/kg of plant), while for Q. rysophylla, it was methanolic extract (19,875.66 ± 2754.01 QE/kg of plant). In the DPPH radical scavenging activity, Q. sartorii showed the highest percentage of inhibition in the methanolic extract (81.14 ± 1.7%), while in Q. rysophylla, it was the ethanolic extract (82.60 ± 2.7%). In the antimicrobial tests, inhibition halos were obtained in the strains Acinetobacter baumannii and Staphylococcus aureus of both species. All this gives a guideline to comprehensively elucidate the metabolites present in these two species for further study and application in the dispute against pathogenic bacteria or in diseases related to the imbalance of reactive oxygen species (ROS).
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(This article belongs to the Special Issue Plant Natural Compounds: From Discovery to Application)
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Tuning Up In Vitro Growth and Development of Cannabis sativa: Recent Advances in Micropropagational Approach
by
S. M. Ahsan, Md. Injamum-Ul-Hoque, Ashim Kumar Das, Shifa Shaffique, Mehedi Hasan, Sang-Mo Kang, In-Jung Lee and Hyong Woo Choi
Appl. Biosci. 2025, 4(1), 12; https://doi.org/10.3390/applbiosci4010012 - 1 Mar 2025
Abstract
Cannabis sativa is used for multiple purposes, notably for its medicinal properties. It produces various secondary metabolites, including cannabinoids, terpenes, and flavonoids, which have therapeutic value and typically produce high amounts in female plants. The growth of the global cannabis market has led
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Cannabis sativa is used for multiple purposes, notably for its medicinal properties. It produces various secondary metabolites, including cannabinoids, terpenes, and flavonoids, which have therapeutic value and typically produce high amounts in female plants. The growth of the global cannabis market has led to intensive breeding efforts to develop elite cultivars with enhanced secondary metabolite profiles. As a dioecious and anemophilous plant, it produces staminate and pistillate inflorescences on separate plants and relies on wind for pollination, rendering traditional propagation methods challenging owing to high genetic recombination in progeny. Consequently, asexual propagation (micropropagation) is commonly employed to maintain female clones entirely. Micropropagation/direct organogenesis is a tissue culture technique that produces numerous disease-free clone plants in vitro more rapidly than traditional rooted cuttings. Factors such as sterilization, hormonal balance, explant type, nutrient additives, carbon source, pH, and environment influence the success of cultivar-specific micropropagation. In this review, we discussed how these factors affect cannabis micropropagation based on recent findings, emphasizing the importance of optimizing cultivar-specific protocols for long-term germplasm conservation and efficient breeding based on a mechanistic background.
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(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2024)
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Open AccessArticle
SALM: A Unified Model for 2D and 3D Region of Interest Segmentation in Lung CT Scans Using Vision Transformers
by
Hadrien T. Gayap and Moulay A. Akhloufi
Appl. Biosci. 2025, 4(1), 11; https://doi.org/10.3390/applbiosci4010011 - 17 Feb 2025
Abstract
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Accurate segmentation of Regions of Interest (ROI) in lung Computed Tomography (CT) is crucial for early lung cancer diagnosis and treatment planning. However, the variability in size, shape, and location of lung lesions, along with the complexity of 3D spatial relationships, poses significant
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Accurate segmentation of Regions of Interest (ROI) in lung Computed Tomography (CT) is crucial for early lung cancer diagnosis and treatment planning. However, the variability in size, shape, and location of lung lesions, along with the complexity of 3D spatial relationships, poses significant challenges. In this work, we propose SALM (Segment Anything in Lung Model), a deep learning model for 2D and 3D ROI segmentation. SALM leverages Vision Transformers, proposing an adaptation of positional encoding functions to effectively capture spatial relationships in both 2D slices and 3D volumes using a single, unified model. Evaluation on the LUNA16 dataset demonstrated strong performance in both modalities. In 2D segmentation, SALM achieved a Dice score of 93% on 124,662 slices. For 3D segmentation using 174 3D images from the same dataset, SALM attained a Dice score of 81.88%. We also tested SALM on an external database (PleThora) on a subset of 255 pulmonary CT from diseased patients, where it achieved a Dice score of 78.82%. These results highlight SALM’s ability to accurately segment lung ROI in both 2D and 3D, demonstrating its potential to improve the accuracy and efficiency of computer-aided diagnosis for lung cancer.
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Open AccessArticle
Isolation of Bacteriophages Lytic to Fusobacterium necrophorum Subspecies necrophorum from Bovine Ruminal Fluid and City Sewage
by
Sydney E. Schnur, Alyssa Deters, Tara Gaire, Victoriya Volkova, Biswajit Biswas, Daniel U. Thomson and Tiruvoor G. Nagaraja
Appl. Biosci. 2025, 4(1), 10; https://doi.org/10.3390/applbiosci4010010 - 10 Feb 2025
Abstract
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Fusobacterium necrophorum subspecies necrophorum, a resident of the rumen, is the causative agent of bovine liver abscesses. Currently, tylosin, a macrolide, is used in the feed to reduce liver abscesses. Because macrolides are medically important antibiotics, their use in food animal production
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Fusobacterium necrophorum subspecies necrophorum, a resident of the rumen, is the causative agent of bovine liver abscesses. Currently, tylosin, a macrolide, is used in the feed to reduce liver abscesses. Because macrolides are medically important antibiotics, their use in food animal production is of public health concern. There is significant interest in finding antimicrobial alternatives. Bacteriophages that lyse subsp. necrophorum have the potential to replace tylosin. Our objective was to isolate bacteriophages lytic to subsp. necrophorum. Pooled ruminal fluid from slaughtered cattle and pooled sewage samples were collected and incubated overnight with lysine, and subsp. necrophorum strains and filtrates were spotted on F. necrophorum lawns. Phage plaques were harvested and purified. Bacteriophage isolation frequencies were compared between sample types, sampling dates, and necrophorum strains. Overall relative frequency of isolated bacteriophages lytic to subsp. necrophorum was 17.1%. The frequency of bacteriophage isolation ranged from 0 to 25.4% for ruminal fluid, and from 13.7 to 32.0% for sewage. Isolation frequency was significantly higher in sewage than in ruminal fluid samples (p < 0.01). Isolation rates varied significantly between necrophorum strains. Sewage was a rich source of bacteriophages lytic to necrophorum, which have the potential to be used to prevent liver abscesses.
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