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Applied Biosciences
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Feature Papers in Applied Biosciences 2023
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Feature Papers in Applied Biosciences 2023

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

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 30715

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editor

Prof. Dr. Robert Henry

E-Mail Website
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
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Many advances in the technologies that underpin biosciences have accelerated the potential for the application of novel approaches to the major challenges of human health and wellbeing. 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 the Special Issue entitled “Feature Papers in Applied Biosciences 2023” and 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) for 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;
  • 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;
  • Advances in rapid diagnostics;
  • Production of biomaterials and biofuels;
  • Advanced biomanufacturing.

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

Prof. Dr. Robert Henry
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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.

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Related Special Issue

Published Papers (10 papers)

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Research

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21 pages, 3758 KiB  
Article
Determination of Target Crop Loads for Maximising Fruit Quality and Return Bloom in Several Apple Cultivars
by Sally A. Bound
Appl. Biosci. 2023, 2(4), 586-606; https://doi.org/10.3390/applbiosci2040037 - 1 Nov 2023
Cited by 1 | Viewed by 1244
Abstract
In apple (Malus domestica), the level and timing of crop load have a major impact on the final fruit size and can also play a role in optimising internal fruit quality. Ideal crop loads vary with cultivar, but very few cultivars [...] Read more.
In apple (Malus domestica), the level and timing of crop load have a major impact on the final fruit size and can also play a role in optimising internal fruit quality. Ideal crop loads vary with cultivar, but very few cultivars have recommended crop load targets that consider the effect of crop load on both return bloom and fruit quality. To address this issue, studies examining a range of crop loads and thinning times were undertaken on several apple cultivars. Return bloom and multiple fruit quality parameters were examined. The results of these studies demonstrate positive effects for early thinning, not only on fruit size but also on firmness and soluble solids content. Early-thinned fruit showed higher sugar levels than late-thinned fruit. Previously undemonstrated positive relationships between fruit sugar content and weight and between fruit firmness and weight in both ‘Fuji’ and ‘Delicious’, as well as between fruit sugar content and fruit firmness in ‘Delicious’, indicate that early thinning is a valuable tool in improving fruit quality. The current target crop load recommendations of 4–6 fruit cm−2 trunk cross-sectional area (TCSA) for ‘Fuji’ and 2–4 fruit cm−2 TCSA for ‘Delicious’ are confirmed by this study. New recommendations are proposed for the other cultivars in this study taking into account the impact of crop load on both fruit quality and return bloom. Both ‘Pink Lady’ and ‘Gala’ can support crop loads of up to eight fruit cm−2 TCSA without impacting return bloom, but fruit quality is compromised; hence, lower targets in the range of 4–6 fruit cm−2 TCSA are recommended. Large fruit size and good return bloom can be maintained in ‘Jonagold’ at crop loads of eight fruit cm−2 TCSA, while crop loads of four fruit cm−2 TCSA are suggested for ‘Braeburn’ to sustain regular bearing and good fruit size. Full article
(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2023)
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22 pages, 2255 KiB  
Article
Sequencing, Fast and Slow: Profiling Microbiomes in Human Samples with Nanopore Sequencing
by Yunseol Park, Jeesu Lee and Hyunjin Shim
Appl. Biosci. 2023, 2(3), 437-458; https://doi.org/10.3390/applbiosci2030028 - 17 Aug 2023
Cited by 2 | Viewed by 2293
Abstract
Rapid and accurate pathogen identification is crucial in effectively combating infectious diseases. However, the current diagnostic tools for bacterial infections predominantly rely on century-old culture-based methods. Furthermore, recent research highlights the significance of host–microbe interactions within the host microbiota in influencing the outcome [...] Read more.
Rapid and accurate pathogen identification is crucial in effectively combating infectious diseases. However, the current diagnostic tools for bacterial infections predominantly rely on century-old culture-based methods. Furthermore, recent research highlights the significance of host–microbe interactions within the host microbiota in influencing the outcome of infection episodes. As our understanding of science and medicine advances, there is a pressing need for innovative diagnostic methods that can identify pathogens and also rapidly and accurately profile the microbiome landscape in human samples. In clinical settings, such diagnostic tools will become a powerful predictive instrument in directing the diagnosis and prognosis of infectious diseases by providing comprehensive insights into the patient’s microbiota. Here, we explore the potential of long-read sequencing in profiling the microbiome landscape from various human samples in terms of speed and accuracy. Using nanopore sequencers, we generate native DNA sequences from saliva and stool samples rapidly, from which each long-read is basecalled in real-time to provide downstream analyses such as taxonomic classification and antimicrobial resistance through the built-in software (<12 h). Subsequently, we utilize the nanopore sequence data for in-depth analysis of each microbial species in terms of host–microbe interaction types and deep learning-based classification of unidentified reads. We find that the nanopore sequence data encompass complex information regarding the microbiome composition of the host and its microbial communities, and also shed light on the unexplored human mobilome including bacteriophages. In this study, we use two different systems of long-read sequencing to give insights into human microbiome samples in the ‘slow’ and ‘fast’ modes, which raises additional inquiries regarding the precision of this novel technology and the feasibility of extracting native DNA sequences from other human microbiomes. Full article
(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2023)
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11 pages, 1117 KiB  
Communication
Review of Partial Hybrids between Herbaceous Medicago sativa and Woody Medicago arborea and Their Potential Role in Alfalfa Improvement
by John Irwin and Edwin Bingham
Appl. Biosci. 2023, 2(3), 373-383; https://doi.org/10.3390/applbiosci2030024 - 13 Jul 2023
Viewed by 1411
Abstract
Medicago sativa (2n = 4x = 32) and M. arborea (2n = 4x = 32) were thought to be reproductively isolated until hybrids (Alborea) were produced by sexual reproduction for the first time in 2003 in Wisconsin. The hybrids were asymmetric, at or [...] Read more.
Medicago sativa (2n = 4x = 32) and M. arborea (2n = 4x = 32) were thought to be reproductively isolated until hybrids (Alborea) were produced by sexual reproduction for the first time in 2003 in Wisconsin. The hybrids were asymmetric, at or near 2n = 4x = 32, and with a predominance of the alfalfa genome. Only M. sativa seed parents with reproductive abnormalities, including unreduced eggs, have produced hybrids; where M. arborea has been used as the seed parent, no hybrids have resulted. Pedigree selection within derivatives of the two original M. sativa seed parents (MB and M8) has been successful in increasing the frequency of hybrids produced. While Alborea individuals more closely resemble M. sativa, a number of M. arborea-specific traits have been observed across different hybrid individuals. These include single-coil flat pods, large seeds, yellow flowers, indeterminate growth, a minimal crown, lodging, frost resistance, and anthracnose resistance. These M. arborea traits have the potential to restructure alfalfa to increase its versatility and utilisation. There is emerging evidence from North and South America and Australia that some Alborea selections have the capacity to complement adapted alfalfa cultivars for yield. Work is continuing to introgress M. arborea traits of value into alfalfa. Full article
(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2023)
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19 pages, 1786 KiB  
Article
Exploring the Synergistic Impacts of Cover Crops and Fertilization on Soil Microbial Metabolic Diversity in Dryland Soybean Production Systems Using Biolog EcoPlates
by Durga P. M. Chinthalapudi, Sapna Pokhrel, William L. Kingery, Mark W. Shankle and Shankar Ganapathi Shanmugam
Appl. Biosci. 2023, 2(3), 328-346; https://doi.org/10.3390/applbiosci2030022 - 6 Jul 2023
Cited by 6 | Viewed by 2273
Abstract
The metabolic diversity of soil microbiota embodies diverse functional capabilities that support ecosystem resilience, driving essential biogeochemical processes and facilitating the optimization of sustainable agricultural systems. Integrating cover crops into agricultural systems cultivates a diverse array of metabolic activities among soil microbes, synergistically [...] Read more.
The metabolic diversity of soil microbiota embodies diverse functional capabilities that support ecosystem resilience, driving essential biogeochemical processes and facilitating the optimization of sustainable agricultural systems. Integrating cover crops into agricultural systems cultivates a diverse array of metabolic activities among soil microbes, synergistically enhancing ecosystem services and bolstering soil health for sustainable and productive farming practices. In an effort to gain deeper insights and expand our knowledge, we conducted a study examining the effects of cover crops and fertilizer sources, thereby shedding light on their combined impacts on the metabolic activity dynamics of soil microbial communities. In this investigation, we employed a split-plot design with two factors: (a) cover crop with three solo cover crop species—Cereal rye (Secale cereale), wheat (Triticum aestivum), hairy vetch (Vicia villosa), and one mixture of mustard (Brassica rapa) and cereal rye (Secale cereale) (CC-mix), (b) Fertilizer source includes poultry litter, chemical fertilizer, and no-fertilizer treatments. We assessed the metabolic potential of soil microbiota by using carbon substrates utilizing Biolog EcoPlates. The findings revealed that the plots with CC-mix treatment exhibited greater metabolic diversity compared to the other treatments, while among the fertilizer sources, poultry litter demonstrated higher metabolic activity. Furthermore, both treatment factors predominantly metabolized carbohydrates and polymers compared to other carbon substrate categories. The principal component analysis accounted for 46.4% of the variance, collectively represented by PC1 and PC2, emphasizing the substantial contributions of carbohydrates, amino acids, and carboxylic acids to the observed metabolic diversity. Canonical correspondence analysis revealed that pH had positively correlated with microbial functional diversity, whereas total carbon (TC), total nitrogen (TN), and water-stable aggregates (WSA) showed a negative correlation. In conclusion, cover cropping and type of fertilizer source had a notable impact on soil microbial functional diversity, with the cover crop mixture exhibiting a more pronounced influence than the individual cover crop treatments. Full article
(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2023)
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14 pages, 2172 KiB  
Article
Coupled Biogas and Fiber Production from Agricultural Residues and Energy Crops with Steam Explosion Treatment
by Benedikt Hülsemann, Marian Baumgart, Leonhard Lenz, Elviliana, Marie Föllmer, Gregor Sailer, Konstantin Dinkler and Hans Oechsner
Appl. Biosci. 2023, 2(2), 278-291; https://doi.org/10.3390/applbiosci2020019 - 1 Jun 2023
Viewed by 1752
Abstract
The global demand for packaging materials and energy is constantly increasing, requiring the exploration of new concepts. In this work, we presented a bioeconomic concept that uses steam explosion and phase separation to simultaneously generate fibers for the packaging industry and biogas substrate [...] Read more.
The global demand for packaging materials and energy is constantly increasing, requiring the exploration of new concepts. In this work, we presented a bioeconomic concept that uses steam explosion and phase separation to simultaneously generate fibers for the packaging industry and biogas substrate for the energy sector. The concept focused on fiber-rich residues and fiber-rich ecological energy crops from agriculture. Feasibility of the concept in the laboratory using feedstocks, including Sylvatic silphia silage, Nettle silage, Miscanthus, Apple pomace, Alfalfa stalks, and Flax shives was confirmed. Our results showed that we were able to separate up to 26.2% of the methane potential while always extracting a smaller percentage of up to 17.3% of organic dry matter (ODM). Specific methane yields of 297–486 LCH4 kgODM−1 in the liquid and 100–286 LCH4 kgODM−1 in the solid phase were obtained. The solid phases had high water absorption capacities of 216–504% due to the steam explosion, while the particle size was not significantly affected. The concept showed high potential, especially for undried feedstock. Full article
(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2023)
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14 pages, 2582 KiB  
Article
Seed Morpho-Anatomy and Germination Enhancement of the Australian Native Species Lomandra longifolia Labill. and L. hystrix (R.Br.) L.R. Fraser & Vickery
by Fernanda Caro Beveridge, Alwyn Williams, Robyn Cave, Sundaravelpandian Kalaipandian and Steve W. Adkins
Appl. Biosci. 2023, 2(2), 222-235; https://doi.org/10.3390/applbiosci2020016 - 16 May 2023
Viewed by 1538
Abstract
Lomandra species are an important understory component of many Australian native ecosystems, contributing to the floristic richness and stabilizing soils. However, a limited understanding of their germination biology currently hinders their efficient use in seed-based restoration and ornamental plant production. The present study [...] Read more.
Lomandra species are an important understory component of many Australian native ecosystems, contributing to the floristic richness and stabilizing soils. However, a limited understanding of their germination biology currently hinders their efficient use in seed-based restoration and ornamental plant production. The present study investigated Lomandra longifolia and L. hystrix diaspore morpho-anatomy and evaluated different mechanical and/or chemical treatments (nicking, leaching, smoke water and gibberellic acid [GA3]) and under light or dark conditions to enhance germination. Embryos of both species were small and linear with a low embryo to seed ratio (<0.45). Germination rates of both species were significantly hastened by leaching seeds in running water for 36 h as compared to a non-leached seed. The results suggest that pre-treating both Lomandra species by leaching could maximize the effectiveness of seed used by resulting in faster, more uniform and, therefore, reliable germination of these species. Finally, seeds of L. longifolia had low final germination (<40%), with a high presence of viable but dormant seeds. The ecological cues that promote germination in nature for both species should be further examined. Full article
(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2023)
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11 pages, 290 KiB  
Article
Caffeic Acid and Biopesticides Interactions for the Control of Storage Beetles
by Chrysanthi Zarmakoupi, Konstantinos Mpistiolis, George Pantazis, Panagiota Psatha, Despoina Dimitriadi, Foteini Kitsiou, Panagiotis Eliopoulos, George Patakioutas and Spiridon Mantzoukas
Appl. Biosci. 2023, 2(2), 211-221; https://doi.org/10.3390/applbiosci2020015 - 8 May 2023
Viewed by 1813
Abstract
Infestations of stored-product pests cause significant losses of agricultural produce every year. Despite various environmental and health risks, chemical insecticides are now a ready-to-use solution for pest control. Against this background and in the context of Integrated Pest Management research, the present study [...] Read more.
Infestations of stored-product pests cause significant losses of agricultural produce every year. Despite various environmental and health risks, chemical insecticides are now a ready-to-use solution for pest control. Against this background and in the context of Integrated Pest Management research, the present study focuses on the potential insecticidal effect of caffeic acid at five different concentrations (250, 500, 750, 1500 and 3000 ppm), and their combination with Cydia pomonella Granulovirus (CpGV), Bacillus thuringiensis subsp. tenebrionis and Beauveria bassiana strain GHA on three major insect stored-product beetle species, Tribolium confusum (Coleoptera: Tenebrionidae), Cryptolestes ferrugineus (Coleoptera: Laemophloeidae) and Trogoderma granarium Everts (Coleoptera: Dermestidae). Treatment efficacy was expressed as mortality in relation to exposure time and adult species number. Compared to the control, the results showed a clear dose-dependent pesticidal activity, expressed as significant adult mortality at a high-dose application, although some of the combinations of caffeic acid concentrations with the other substances acted positively (synergistically and additively) and some negatively. Based on our results, bioinsecticides can be combined with plant compounds such as caffeic acid and be integrated with other modern IPM tools in storage facilities. Full article
(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2023)

Review

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31 pages, 1223 KiB  
Review
The Integration of Artificial Intelligence into Clinical Practice
by Vangelis D. Karalis
Appl. Biosci. 2024, 3(1), 14-44; https://doi.org/10.3390/applbiosci3010002 - 1 Jan 2024
Cited by 26 | Viewed by 13050
Abstract
The purpose of this literature review is to provide a fundamental synopsis of current research pertaining to artificial intelligence (AI) within the domain of clinical practice. Artificial intelligence has revolutionized the field of medicine and healthcare by providing innovative solutions to complex problems. [...] Read more.
The purpose of this literature review is to provide a fundamental synopsis of current research pertaining to artificial intelligence (AI) within the domain of clinical practice. Artificial intelligence has revolutionized the field of medicine and healthcare by providing innovative solutions to complex problems. One of the most important benefits of AI in clinical practice is its ability to investigate extensive volumes of data with efficiency and precision. This has led to the development of various applications that have improved patient outcomes and reduced the workload of healthcare professionals. AI can support doctors in making more accurate diagnoses and developing personalized treatment plans. Successful examples of AI applications are outlined for a series of medical specialties like cardiology, surgery, gastroenterology, pneumology, nephrology, urology, dermatology, orthopedics, neurology, gynecology, ophthalmology, pediatrics, hematology, and critically ill patients, as well as diagnostic methods. Special reference is made to legal and ethical considerations like accuracy, informed consent, privacy issues, data security, regulatory framework, product liability, explainability, and transparency. Finally, this review closes by critically appraising AI use in clinical practice and its future perspectives. However, it is also important to approach its development and implementation cautiously to ensure ethical considerations are met. Full article
(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2023)
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17 pages, 1275 KiB  
Review
Crossiella, a Rare Actinomycetota Genus, Abundant in the Environment
by Tamara Martin-Pozas, Jose Luis Gonzalez-Pimentel, Valme Jurado, Leonila Laiz, Juan Carlos Cañaveras, Angel Fernandez-Cortes, Soledad Cuezva, Sergio Sanchez-Moral and Cesareo Saiz-Jimenez
Appl. Biosci. 2023, 2(2), 194-210; https://doi.org/10.3390/applbiosci2020014 - 6 May 2023
Cited by 9 | Viewed by 2944
Abstract
The genus Crossiella contains two species, C. equi, causing nocardioform placentitis in horses, and C. cryophila, an environmental bacterium. Apart from C. equi, which is not discussed here, environmental Crossiella is rarely reported in the literature; thus, it has not [...] Read more.
The genus Crossiella contains two species, C. equi, causing nocardioform placentitis in horses, and C. cryophila, an environmental bacterium. Apart from C. equi, which is not discussed here, environmental Crossiella is rarely reported in the literature; thus, it has not been included among “rare actinobacteria”, whose isolation frequency is very low. After C. cryophila, only five reports cover the isolation of Crossiella strains. However, the frequency of published papers on environmental Crossiella has increased significantly in recent years due to the extensive use of next-generation sequencing (NGS) and a huge cascade of data that has improved our understanding of how bacteria occur in the environment. In the last five years, Crossiella has been found in different environments (caves, soils, plant rhizospheres, building stones, etc.). The high abundance of Crossiella in cave moonmilk indicates that this genus may have an active role in moonmilk formation, as evidenced by the precipitation of calcite, witherite, and struvite in different culture media. This review provides an overview of environmental Crossiella, particularly in caves, and discusses its role in biomineralization processes and bioactive compound production. Full article
(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2023)
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Other

Jump to: Research, Review

10 pages, 3987 KiB  
Perspective
The Chaperone Hsp90, a Key Player in Salivary Gland Tumorigenesis
by Charbel A. Basset, Inaya Hajj Hussein, Abdo R. Jurjus, Francesco Cappello, Everly Conway de Macario, Alberto J. L. Macario and Angelo Leone
Appl. Biosci. 2023, 2(4), 607-616; https://doi.org/10.3390/applbiosci2040038 - 7 Nov 2023
Viewed by 1206
Abstract
The chaperone system (CS) is emerging as a key multistage participant in carcinogenesis. The CS chief components are the molecular chaperones (some of which are named heat shock proteins or Hsp), which are typically cytoprotective but if abnormal in structure, location, or quantity, [...] Read more.
The chaperone system (CS) is emerging as a key multistage participant in carcinogenesis. The CS chief components are the molecular chaperones (some of which are named heat shock proteins or Hsp), which are typically cytoprotective but if abnormal in structure, location, or quantity, can become etiopathogenic and cause diseases, known as chaperonopathies, including some cancers. For example, abnormal Hsp90 expression is associated with tumorigenesis and poor prognosis. Hsp90 is positioned at the center of several key oncogenic pathways by stabilizing and activating oncogenic kinases responsible for driving cell proliferation and survival. Consequently, inhibition of Hsp90 is being investigated as a possible anti-cancer strategy and some results are encouraging. However, the 5-year survival rate for patients suffering from salivary gland carcinomas is still unsatisfactory. Because of the rarity of these malignancies, they may have been overlooked and understudied and, thus, novel therapies (e.g., inhibition of CS components like Hsp90 and others) are urgently needed. In this review, we also summarize the histopathological quantitative patterns and the intra- and extra-cellular location characteristics of Hsp90 in tumors of salivary glands, pointing to their potential for differential diagnosis, prognostication, and patient monitoring. Full article
(This article belongs to the Special Issue Feature Papers in Applied Biosciences 2023)
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