Feature Papers in Applied Biosciences 2024

A special issue of Applied Biosciences (ISSN 2813-0464).

Deadline for manuscript submissions: closed (31 December 2024) | Viewed by 14105

Special Issue Editors


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Guest Editor
1. Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia
2. ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, QLD 4072, Australia
Interests: genomics; transcriptomics; plant adaptation; wild crop relatives; output traits
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Guest Editor
Department of Chemistry and Chemical Biology, College of Sciences, Northeastern University, Boston, MA 02115, USA
Interests: microbial ecology; biotechnology; growth kinetics and stoichiometry; fermentation; mathematical models of microbial growth; genome-scale metabolic reconstructions; history of microbiology
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Guest Editor
Department Medical Physics, School of Health Sciences, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
Interests: optical methods for tissue diagnostics; bio-molecular spectroscopy; x-ray diffraction; computational biophysics and drug design; molecular modeling
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Many advances in technologies underpinning biosciences have accelerated the potential for the application of novel approaches to the major challenges of human health and well-being. It is important that those developing these technologies connect with those looking to apply them to deliver new solutions. Applied Biosciences (ISSN 2813-0464) has the opportunity to contribute to this knowledge exchange.

We are pleased to announce this Special Issue focusing on new advances in the biotechnology, biosciences and bioengineering of plants, animals and humans.

We welcome the submission of manuscripts from Editorial Board Members and from outstanding scholars invited by the Editorial Board Members and the Editorial Office. The following are suggested (as examples of options) as submission topics:

  • Advances in drug discovery;
  • Microscopy and molecular imaging technology developments;
  • Advances in antibody engineering;
  • Novel bioassay technologies;
  • New bioinformatics tools;
  • Recent applications of genome engineering in plants or animals;
  • Cell engineering;
  • Enzyme engineering;
  • Applications of nanobiotechnology;
  • Advances in the production and use of biopolymers;
  • Novel vaccine technologies/mRNA vaccines;
  • Algal products and production systems;
  • Advances in long-read DNA sequencing;
  • Biomass processing technologies;
  • Production of biomaterials and biofuels;
  • Advanced biomanufacturing;
  • Microbial biotechnology.

We hope you can participate in this Special Issue and look forward to receiving your contributions.

Prof. Dr. Robert Henry
Dr. Nicolai S. Panikov
Dr. Nikolaos Kourkoumelis
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Applied Biosciences is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • advances in drug discovery
  • microscopy and molecular imaging technology developments
  • advances in antibody engineering
  • novel bioassay technologies
  • new bioinformatics tools
  • recent applications of genome engineering in plants or animals
  • cell engineering
  • enzyme engineering
  • applications of nanobiotechnology
  • advances in the production and use of biopolymers
  • novel vaccine technologies/mRNA vaccines
  • algal products and production systems
  • advances in long-read DNA sequencing
  • biomass processing technologies
  • production of biomaterials and biofuels
  • advanced biomanufacturing
  • microbial biotechnology

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Related Special Issue

Published Papers (11 papers)

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Research

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19 pages, 4092 KiB  
Article
Effect of Integrated Crop–Livestock Systems on Soil Properties and Microbial Diversity in Soybean Production
by Namita Sinha, Brett R. Rushing, Aniruddha Acharya and Shankar Ganapathi Shanmugam
Appl. Biosci. 2024, 3(4), 484-502; https://doi.org/10.3390/applbiosci3040031 - 8 Nov 2024
Viewed by 1014
Abstract
Integrated crop and livestock systems (ICLSs) have been considered an important management-based decision to improve soil health by carbon sequestration. A two-year study (2019–2021) at CPBES in Newton, MS, was conducted to evaluate the effect of an ICLS on soil microbial diversity in [...] Read more.
Integrated crop and livestock systems (ICLSs) have been considered an important management-based decision to improve soil health by carbon sequestration. A two-year study (2019–2021) at CPBES in Newton, MS, was conducted to evaluate the effect of an ICLS on soil microbial diversity in the southeastern region of the USA, representing agroclimatic conditions that are warm and humid. Amplicons targeting bacterial 16S rRNA genes and fungal ITS2 regions were sequenced. Taxonomic assignment and characterization of microbial diversity were performed using QIIME2®. Soil fungal diversity pattern showed significant difference (alpha diversity, p = 0.031 in 2020 and beta diversity, p = 0.037 in 2021). In contrast, no significant differences were observed in bacterial diversity. However, there were several beneficial bacterial phyla, such as Proteobacteria and Actinobacteria, and fungal phyla such as Ascomycota, which were dominant in both years and did not show significant differences due to cover crop treatments. Canonical Correspondence Analysis (CCA) and Mantel test showed significant influence on fungal diversity due to carbon (rm = 0.2581, p = 0.022), nitrogen (rm = 0.2921, p = 0.0165), and electrical conductivity (rm = 0.1836, p = 0.0583) in 2021, and on bacterial diversity due to EE-GRSP (rm = 0.22, p = 0.02) in 2020. However, the results showed that there were no significant differences between the cover crop treatments that were consistent over a two-year study period. However, the mix of different cover crops such as oats (Avena sativa L.), crimson clover (Trifolium incarnatum L.), and tillage radish (Raphanus sativus L.) demonstrated higher positive correlation and lower negative correlation with different bacterial and fungal phyla. Long term study of ICLS is suggested to understand the shift in microbiome that would help in understanding the role of cover crops and grazing in improving crop production sustainably. Full article
(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2024)
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13 pages, 2694 KiB  
Article
Orthotic Thermoplastic Demonstrates a Similar Contamination Potential with Bacillus Bacteria Recovered from Thermoplastic Radiation Therapy Patient Masks
by Catherine W. Brock, Dev V. Mehta and Terrence J. Ravine
Appl. Biosci. 2024, 3(2), 250-262; https://doi.org/10.3390/applbiosci3020017 - 1 Jun 2024
Viewed by 1152
Abstract
Thermoplastics used to construct a variety of patient medical devices can become contaminated by harmful bacteria. We investigated whether two different Bacillus species recovered from patient radiation therapy thermoplastic masks could similarly contaminate thermoplastic material used to construct patient orthoses (splints). Bacillus bacteria [...] Read more.
Thermoplastics used to construct a variety of patient medical devices can become contaminated by harmful bacteria. We investigated whether two different Bacillus species recovered from patient radiation therapy thermoplastic masks could similarly contaminate thermoplastic material used to construct patient orthoses (splints). Bacillus bacteria form dormant spores, which have been shown to enhance its attachment to thermoplastics. Bacterial attachment and recovery were examined using an orthotic thermoplastic with an anti-stick coating being compared to uncoated material used in radiation therapy applications. Triplicate sample squares were seeded with a saline suspension of either B. cereus (MAB03F) or B. megaterium (DAB01F) containing a similar number of spores. Squares were subsequently sampled at 1 h, 1 week, 2 weeks, 4 weeks, and 8 weeks. The number of recovered bacteria was counted. Differences in material hydrophobicity were determined by water contact angle analysis. Both Bacillus species attached to each material within 1 h, and their spores were recovered at 8 weeks. However, a decreasing trend in adhesion, over time, was noted to the coated material with an opposite increasing trend in the uncoated material. Decreased Bacillus species spore adhesion to coated material with a lower hydrophobicity suggests a greater potential for spore transfer to patients wearing contaminated orthoses. Full article
(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2024)
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Review

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45 pages, 990 KiB  
Review
Enzymatic Oxidants, Antioxidants, and Inflammatory Bowel Disease
by R. Steven Esworthy
Appl. Biosci. 2025, 4(2), 19; https://doi.org/10.3390/applbiosci4020019 - 1 Apr 2025
Viewed by 197
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2024)
26 pages, 3130 KiB  
Review
Advancements in Nanotechnology for Targeted and Controlled Drug Delivery in Hematologic Malignancies: Shaping the Future of Targeted Therapeutics
by Abdurraouf Mokhtar Mahmoud and Clara Deambrogi
Appl. Biosci. 2025, 4(1), 16; https://doi.org/10.3390/applbiosci4010016 - 5 Mar 2025
Viewed by 736
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2024)
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17 pages, 4490 KiB  
Review
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
Viewed by 590
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2024)
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27 pages, 747 KiB  
Review
Lactiplantibacillus plantarum, the Integral Member of Vegetable Fermentations
by Spiros Paramithiotis
Appl. Biosci. 2025, 4(1), 7; https://doi.org/10.3390/applbiosci4010007 - 5 Feb 2025
Viewed by 861
Abstract
Lactiplantibacillus plantarum is omnipresent in vegetable fermentations. Its large metabolic capacity and its ability to adapt to the fermenting microenvironment enable this species, in many cases, to dominate the microecosystem and drive the fermentation. In addition, its metabolic capacity enables it to produce [...] Read more.
Lactiplantibacillus plantarum is omnipresent in vegetable fermentations. Its large metabolic capacity and its ability to adapt to the fermenting microenvironment enable this species, in many cases, to dominate the microecosystem and drive the fermentation. In addition, its metabolic capacity enables it to produce bioactive compounds of great interest for human health. These attributes have directed research for many decades. The widespread application of next-generation sequencing approaches has enabled the genotypic verification of the phenotypically assessed attributes and supplemented them with novel insights, justifying the characterization of a multifunctional tool that has been awarded to this species. However, there are still issues that need to be properly addressed in order to improve our understanding of the microecosystem functionality and to enhance our knowledge regarding the capacities of this species. The aim of the present article is to collect and critically discuss the available information on Lp. plantarum subsistence in vegetable fermentations. Full article
(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2024)
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13 pages, 745 KiB  
Review
Does the Use of Two Major Opioids Have an Impact on Improving Pain Treatment and Quality of Life in Cancer Patients?—A Literature Review
by Shirley Duarte, João Rocha-Neves, Marília Dourado and Hugo Ribeiro
Appl. Biosci. 2025, 4(1), 3; https://doi.org/10.3390/applbiosci4010003 - 7 Jan 2025
Viewed by 1020
Abstract
Cancer pain is a highly prevalent problem and one of the most distressing symptoms in cancer patients. The management of cancer pain is one of the most significant challenges in the care of these patients. Cancer pain must be treated quickly and effectively [...] Read more.
Cancer pain is a highly prevalent problem and one of the most distressing symptoms in cancer patients. The management of cancer pain is one of the most significant challenges in the care of these patients. Cancer pain must be treated quickly and effectively as it affects the quality of life and reduces the patient’s life expectancy. Major opioids are recognized by the World Health Organization (WHO) as first-line treatment for moderate to severe cancer pain, but their use is often hampered by individual variations, comorbidities, and complications associated with cancer. Since the simultaneous use of two major opioids has become frequent, a narrative review was conducted, whose main objectives were to evaluate whether the combination of two major opioids improves pain and quality of life in cancer patients, considering their pharmacodynamic and pharmacokinetic properties and evaluate the impact of this combination on the frequency and intensity of side effects. The search for information was carried out in evidence-based medicine databases, namely PubMed/MEDLINE, Cochrane Library, Database of Abstracts of Reviews of Effects, National Guideline Clearinghouse, NHS Evidence and Index das Revistas Médicas Portuguesas using the MeSH terms “opioids” and “quality of life”. Articles and documents published between 1 January 2010 and 1 June 2023, in English, Portuguese and Spanish, were considered, including original articles, meta-analyses, systematic reviews and clinical guidelines. A total of 342 articles were retrieved and of these, only 13 were selected for full reading. The combination of opioids is based on the principle that different opioids act through different mechanisms, which can reduce dose-related adverse effects. Simultaneous use of two major opioids may allow for more modest increases in the equivalent dose of the second opioid, providing better pain control and reduced side effects such as nausea, vomiting, and constipation. More studies on the combination of opioids are needed to improve cancer pain treatment. The lack of personalized therapies limits the effectiveness of opioids, and variability in treatment responses requires individualized approaches. Personalized medicine, based on pharmacogenomics, is one of the most promising strategies to optimize pain relief and reduce adverse effects. Full article
(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2024)
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40 pages, 1375 KiB  
Review
Application of Thermodynamic Methods to the Study of Plant Biomass and Its Components—A Review
by Ioelovich Michael
Appl. Biosci. 2024, 3(4), 577-616; https://doi.org/10.3390/applbiosci3040036 - 23 Dec 2024
Viewed by 804
Abstract
This article describes the basics of chemical thermodynamics and its application to the study of plant biomass and its main components, cellulose, hemicelluloses, lignin, etc. The energy potential of various biomass types, as well as biomass-based solid, liquid, and gaseous biofuels, is determined. [...] Read more.
This article describes the basics of chemical thermodynamics and its application to the study of plant biomass and its main components, cellulose, hemicelluloses, lignin, etc. The energy potential of various biomass types, as well as biomass-based solid, liquid, and gaseous biofuels, is determined. A method of additive contributions of combustion enthalpies of main components is proposed to calculate the combustion enthalpy of biomass samples. It is also established that the potential of thermal energy of the initial biomass is higher than the energy potential of secondary biofuels released from this biomass. The thermodynamic functions of plant biopolymers are calculated. Moreover, the thermodynamic stability of various crystalline allomorphs of cellulose and amorphous cellulose is studied. The melting enthalpies of crystallites with different types of crystalline structures are estimated. A thermochemical method for determining the degree of crystallinity of cellulose is proposed. The most important biomass components are cellulose and other polysaccharides. The thermodynamics of the enzymatic hydrolysis of polysaccharides and their conversion into glucose are described. In addition, the thermodynamic analysis of the conversion process of glucose into bioethanol is performed. Considerable attention is also paid to the thermochemistry of cellulose alkalization, etherification, and esterification. Full article
(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2024)
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14 pages, 642 KiB  
Review
A Short Review of Second-Generation Isobutanol Production by SHF and SSF
by Hironaga Akita and Akinori Matsushika
Appl. Biosci. 2024, 3(3), 296-309; https://doi.org/10.3390/applbiosci3030020 - 8 Jul 2024
Cited by 1 | Viewed by 1588
Abstract
As isobutanol exhibits higher energy density and lower hygroscopicity than ethanol, it is considered a better candidate biofuel. The sustainable supply of inedible biomass and lack of competition with the food supply have stimulated significant worldwide interest in the production of isobutanol from [...] Read more.
As isobutanol exhibits higher energy density and lower hygroscopicity than ethanol, it is considered a better candidate biofuel. The sustainable supply of inedible biomass and lack of competition with the food supply have stimulated significant worldwide interest in the production of isobutanol from this resource. Both separate hydrolysis and fermentation (SHF) and simultaneous saccharification and fermentation (SSF) have been applied to isobutanol production to effectively utilize inedible biomass as a feedstock. However, both processes have various challenges, including low isobutanol yield and high production costs. This review summarizes the potential of isobutanol as a biofuel, methods for conferring isobutanol productivity, recent experimental studies, and developments in both SHF and SSF with the isobutanol-producing strains. Challenges to increasing the isobutanol yield and various suggestions for improvements to enable commercial production are also discussed. Full article
(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2024)
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20 pages, 1576 KiB  
Review
Sustainable Pulse Proteins: Physical, Chemical and Fermentative Modifications
by Seedhabadee Ganeshan, Nancy Asen, Yingxin Wang, Mehmet Ç. Tülbek and Michael T. Nickerson
Appl. Biosci. 2024, 3(2), 263-282; https://doi.org/10.3390/applbiosci3020018 - 12 Jun 2024
Cited by 1 | Viewed by 2913
Abstract
Pulse proteins are playing significant roles in the alternative protein space due to the demand for foods produced in an environmentally sustainable manner and, most importantly, due to the demand for foods of nutritious value. There has been extensive research to mimic animal-derived [...] Read more.
Pulse proteins are playing significant roles in the alternative protein space due to the demand for foods produced in an environmentally sustainable manner and, most importantly, due to the demand for foods of nutritious value. There has been extensive research to mimic animal-derived meat texture, flavour, mouthfeel, etc. However, there is still the perception that many of the plant-based proteins that have been texturized to mimic meat are still highly processed and contain chemicals or preservatives, reducing their appeal as being healthy and precluding any sustainable benefits. To counter this notion, the biotransformation of pulse proteins using enzymes or fermentation offers unique opportunities. Thus, this review will address the significance of pulse proteins in the alternative protein space and some of the processing aids leading to the isolation and modification of such protein concentrates in a sustainable manner. Fermentation-based valorization of pulse proteins will also be discussed as a “clean label” strategy (further adding to sustainable nutritious plant protein production), although some of the processes like the extensive use of water in submerged fermentation need to be addressed. Full article
(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2024)
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16 pages, 4320 KiB  
Review
Moringa oleifera Seed Cake: A Review on the Current Status of Green Nanoparticle Synthesis
by Nuno Coelho, Alice S. Pereira and Pedro Tavares
Appl. Biosci. 2024, 3(2), 197-212; https://doi.org/10.3390/applbiosci3020013 - 29 Apr 2024
Cited by 1 | Viewed by 1804
Abstract
Growing demands for sustainable and ecological nanoparticle synthesis methods have incentivized the scientific community to develop new approaches to counteract these challenges. Green synthesis resorts to biocomponents obtained from plants, bacteria, fungi, and other organisms to synthesize nanostructures, with beneficial gains in the [...] Read more.
Growing demands for sustainable and ecological nanoparticle synthesis methods have incentivized the scientific community to develop new approaches to counteract these challenges. Green synthesis resorts to biocomponents obtained from plants, bacteria, fungi, and other organisms to synthesize nanostructures, with beneficial gains in the economic and ecological cost associated with the process, simplicity of the process, and resource efficiency. Moringa oleifera, a native plant originally from India with immense nutritive value, has long been used by researchers in the biosynthesis of nanoparticles. Leaves, flowers, bark, and seeds are among the “miracle tree” parts that can be used in nanoparticle green synthesis. Moringa oleifera seed cake, a by-product obtained from defatted seeds, is often overlooked due to its apparent low commercial value. The main objective of this review is to highlight the recent findings reported in the literature on nanoparticles/nanocomposites synthesized with seed cake biocompounds acting as reducing/capping agents. Furthermore, we analyzed the methods currently employed for the extraction of bioactive compounds. Moringa oleifera seed for industrial applications was also addressed. Full article
(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2024)
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