Applied Biosciences doi: 10.3390/applbiosci3010010
Authors: Vasileios Papantzikos Areti Papanikou Vasileios Stournaras Paraskevi Mpeza Spiridon Mantzoukas Georgios Patakioutas
As climate change is an imminent threat to the environment and agriculture, there is an increasing need to find immediate solutions capable of compensating for water deficits even in semi-arid conditions. This study is focused on the evaluation of the vegetative growth of grapevine plants Vitis vinifera L., of the Greek variety “Debina” in a water deficit environment, with the application of two bacterial-based formulations: one with Bacillus amyloliquefaciens (strain QST 713) and one with Sinorhizobium meliloti (strain cepa B2352). The two formulations were tested under rational irrigation (100% of Available Water) and deficit irrigation (57% of AW). After 140 days, plant growth parameters, such as total plant growth length, leaf area, roots, shoots, and leaves dry biomass showed better performance on treatments with plant growth-promoting rhizobacteria (PGPR) formulations under either rational or deficit irrigation conditions. In addition, the metabolic response of the grapevine plants to the deficit irrigation stress, such as the total chlorophyll, leaf relative water, total phenolic, and proline content, proved to be enriched on the treatments with PGPR formulations during this experiment. The two formulations, in conditions of abiotic stress, achieved to almost compensate for the irrigation deficit, boosting the plant metabolism. This study reveals the need for further research on PGPR biostimulants, as this first trial of these formulations on grapevine could be significant in the case of water scarcity and climate change.
]]>Applied Biosciences doi: 10.3390/applbiosci3010009
Authors: Garyfallia Papa Yannis V. Simos Antrea-Maria Athinodorou Konstantinos I. Tsamis Dimitrios Peschos Charalampos Angelidis Periklis Pappas Patra Vezyraki
Flavonoids share a common structural framework that serves as a hallmark indicative of their biological activity. In this study, we investigated the effects of two structurally similar flavonoids, fisetin and morin, through independent and combined in vitro assessments on embryonic mouse cells overexpressing the human 70 kDa heat shock protein (Hsp70) (Tg/Tg) and normal mouse fibroblast cell line (NIH/3T3). The primary objectives were to evaluate the biocompatibility and potential cytotoxicity of these flavonoids, along with assessing the cytoprotective role of Hsp70 in these cellular environments. To address these objectives, we conducted dose- and time-dependent cell survival tests. Additionally, we utilized flow cytometry to detect intracellular reactive oxygen species (ROS) production and to analyze apoptosis and the cell cycle. Throughout the experimental procedures, a notable observation was made: NIH/3T3 normal cells exhibited greater susceptibility compared to Tg/Tg cells when exposed to fisetin and morin. This difference in susceptibility is likely attributed to the robust cytoprotective effect of Hsp70 in Tg/Tg cells. Importantly, both cell lines demonstrated increased sensitivity to fisetin toxicity in comparison to morin, leading to significantly lower cell survival rates. These findings shed light on the differential responses of cell lines to flavonoid exposure, emphasizing the influence of Hsp70 and the distinct impact of fisetin and morin on cell viability.
]]>Applied Biosciences doi: 10.3390/applbiosci3010008
Authors: Priscila Nogueira Bezan Héric Holland Bárbara Ferreira Vercesi Paula Payão Ovídio Livia Maria Cordeiro Simões Alceu Afonso Jordão
Background and objectives: Carbohydrates such as fructooligosaccharides (FOSs) are associated with improved gastrointestinal health and the prevention of excess body fat. We evaluated the long-term effects of high amounts of FOS on metabolic parameters, non-alcoholic fatty liver disease (NAFLD) and short-chain fatty acids (SCFAs). Methods: Sixty C57BL/6 mice received the following diets for four months: control (C), normolipid rich in fiber (F), normolipid supplemented with FOS (FOS), high fat (HL), high fat with high fiber (HLF) and high fat with FOS (HLFOS). We analyzed the animal weight; body composition; food intake; fasting blood glucose; serum and liver lipid profiles; liver and intestinal histologies; malondialdehyde (MDA), hepatic retinol and α-tocopherol; and SCFAs in the feces. Results: Supplementation with FOS in a high-fat diet promoted less body weight gain and reduced liver and retroperitoneal adipose tissue weights compared to HL and HF. FOS prevented NASH and decreased alanine aminotransferase and serum cholesterol levels in experimental animal models of obesity and metabolic syndrome (MS). There were statistical differences found in the dosages of the three main SCFAs in feces (acetic, isobutyric and isovaleric acids). Conclusions: Long-term supplementation with high doses of FOS was effective in reducing weight, adiposity, NAFLD and serum cholesterol in C57BL mice with obesity and MS induced by a high-fat diet.
]]>Applied Biosciences doi: 10.3390/applbiosci3010007
Authors: Andrew Nelson Steven Voinier Jeremy Tran Kristin H. Gilchrist Melvin Helgeson Vincent B. Ho George J. Klarmann
Torn and damaged menisci resulting from trauma are very common knee injuries, which can cause pain and mobility limitations and lead to osteoarthritis. Meniscal injuries can require surgery to repair the tissue damage and restore mobility. Here we describe the biomechanical testing of a 3D-printed meniscus to illustrate methods to determine if it has the strength and durability to effectively repair meniscal tears and restore knee biomechanics. This work was designed to demonstrate the steps needed to test novel meniscus repair devices prior to moving toward animal testing. The first testing step determined the ability of the 3D-printed meniscus to withstand surgical fixation by measuring the suture pull-out force. We show that vertical 2/0 silk or Fiberwire sutures need an average of 1.4 or 1.8 N, respectively, to pull through the meniscus, while horizontal sutures need only 0.7 and 1.2 N, respectively. The next step measured the compressive strength of normal, damaged, and repaired porcine meniscus tissue. Here, we show that meniscectomy decreased the stiffness of meniscus tissue from 26.7 ± 0.85 N to 7.43 ± 0.81 N at 25% strain. Menisci repaired with the 3D-printed tissue restored 66% of the measured force at 25% strain. The final step measured the contact pressures and areas in an ex vivo porcine knee before and after meniscal repair was made with the 3D-printed meniscus tissue. The example 3D-printed meniscus was successfully sutured into the porcine knee joint but failed to restore normal knee contact pressures. This work demonstrates the need for an iterative biomechanical testing process of biomaterial development, 3D-printing optimization, and knee kinematics to develop a durable and functional meniscus repair device. In summary, the methods described here serve as a guide for the functional evaluation of novel meniscus repair devices.
]]>Applied Biosciences doi: 10.3390/applbiosci3010006
Authors: Sara Ricardo-Rodrigues Maria Inês Rouxinol Ana Cristina Agulheiro-Santos Maria Eduarda Potes Marta Laranjo Miguel Elias
Consumers are looking for safer and more natural food options that are produced through natural methods without using synthetic preservatives. They also desire extended shelf life for their food products. Several medicinal and aromatic plants species combine food, spice, aromatic, and medicinal recognized attributes. The essential oils from these plants contain a unique mixture of compounds specific to each plant, showing notable antioxidant and antimicrobial properties. Essential oils are used widely as they are environmentally friendly, non-toxic, and biodegradable substitutes for harsh chemical preservatives. Thyme and clove are aromatic plants commonly used in traditional gastronomy, particularly in meat-based recipes. The preservation effects of these essential oils on fresh meat have not been widely studied. Therefore, the aim of this study is to review the use of thyme and clove essential oils in meat preservation, with particular emphasis on their antioxidant properties to mitigate lipid and protein oxidation. Different strategies have been used to boost the effects of essential oils in foods, which include mixtures of essential oils, encapsulation and nanoemulsification techniques, with or without edible coatings. The final objective is to promote the wide use of essential oils for meat preservation, eventually in combination with other innovative approaches.
]]>Applied Biosciences doi: 10.3390/applbiosci3010005
Authors: Neiton C. Silva Andressa O. Santos Claudio R. Duarte Marcos A. S. Barrozo
Brewer’s spent grain (BSG) is a residue that holds significant potential for various applications. Given its inherently high moisture levels, it becomes imperative to explore methods for preserving it. This study investigates the use of refractance window (RW) for drying BSG. The final moisture content, water activity, and drying kinetics were assessed. Various kinetic models were analyzed, including Lewis, Page, Overhults, Brooker, and Midilli. Employing a central composite design, this study also investigated the effects of the variables temperature (55.9 to 84.1 °C) and drying time (1.6 to 4.4 h) on the quality of the dried product. The quality was assessed based on the content of bioactive compounds: phenolics, flavonoids, citric acid, and ascorbic acid. The results suggest that refractance window (RW) drying can yield a product with reduced moisture content and water activity levels (lower than 10.0% and 0.600, respectively). The phenolic, flavonoid, and citric acid higher contents were found at 70 °C and 3 to 4 h of drying. The best ascorbic acid results were found at 55 to 65 °C after 3 h of drying. The use of RW emerges as an interesting alternative for processing BSG, offering a sustainable approach to better utilize this residue.
]]>Applied Biosciences doi: 10.3390/applbiosci3010004
Authors: Efstratios Christodoulou Georgia-Eirini Deligiannidou Christos Kontogiorgis Constantinos Giaginis Antonios E. Koutelidakis
Increasing evidence indicates that the cultivation of mindful eating, adherence to the Mediterranean lifestyle, and the development of psychological resilience may contribute to the enhancement of overall health and well-being. The purpose of this study was to explore the association between mindful eating and the Mediterranean lifestyle in relation to psychological resilience and the maintenance of a healthy weight. In the framework of a cross-sectional study, 288 individuals voluntarily took part in an online research survey conducted in Greece. Results showed that both mindful eating and the Mediterranean diet were significantly correlated (p < 0.001) with psychological resilience. Multiple regression models identified mindful eating and the Mediterranean diet as predictive factors of psychological resilience (p < 0.001). There was a statistically significant (p < 0.05) intercorrelation between mindful eating, the Mediterranean diet, and psychological resilience. Following the application of multiple regression models, mindful eating and Mediterranean diet were identified as predictive factors of psychological resilience (p < 0.0001). Individuals with a normal Body Mass Index (BMI) displayed stronger adherence to mindful eating and the Mediterranean lifestyle, in contrast to those classified in the overweight and obesity BMI groups. People with higher mindful eating scores had 14% better odds of maintaining their weight loss after a weight-reducing diet than those with a lower mindful eating score (OR: 1.142, 95% CI: 1.084, 1.204, p < 0.0001). In summary, the integration of mindful eating and the Mediterranean lifestyle may represent a feasible approach to bolstering psychological resilience, overall health, and well-being.
]]>Applied Biosciences doi: 10.3390/applbiosci3010003
Authors: Renata F. Saito Camila Maria Longo Machado Ana Luiza Oliveira Lomba Andréia Hanada Otake Maria Cristina Rangel
From an evolutive perspective, tumor cells endure successive turnover upon stress conditions and pressure to adapt to new environments. These cells use exceptional communication skills to share biological information to “survive upon every metabolic cost”. The tumor microenvironment (TME) is a miscellaneous collection of cells, factors, and extracellular vesicles (EVs). EVs are small lipid bilayer-delimited particles derived from cells with sizes ranging from 100 to 1000 nm. Exosomes (<160 nm) are the minor subtype of EVs, originating from the endosomal pathways. The TME also contains “giant” vesicles, microvesicles (100–1000 nm, MV), originated from membrane blebbing. EVs can act as intercellular communication mediators, contributing to many biological processes, by carrying different biomolecules, such as proteins, lipids, nucleic acids, and metabolites. EV secretion can promote either tumor cell survival or manage their stress to death. Tumor-derived EVs transfer adaptative stress signaling to recipient cells, reprograming these cells. Heat shock proteins (HSP) are prominent stress response regulators, specifically carried by exosomes. HSP-loaded EVs reprogram tumor and TME cells to acquire mechanisms contributing to tumor progression and therapy resistance. The intercellular communication mediated by HSP-loaded EVs favors the escape of tumor cells from the endoplasmic reticulum stress, hypoxia, apoptosis, and anticancer therapies. Extracellular HSPs activate and deactivate the immune response, induce cell differentiation, change vascular homeostasis, and help to augment the pre-metastatic niche formation. Here we explore EVs’ mechanisms of HSP transmission among TME cells and the relevance of these intercellular communications in resistance to therapy.
]]>Applied Biosciences doi: 10.3390/applbiosci3010002
Authors: Vangelis D. Karalis
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.
]]>Applied Biosciences doi: 10.3390/applbiosci3010001
Authors: Olavo João Frederico Ramos Junior Karen Souza dos Santos Isabela Ribeiro Grangeira Tavares Gustavo Vieira de Oliveira Thiago Silveira Alvares
Exercise-induced muscle damage is associated with symptoms such as inflammation, delayed-onset muscle soreness, and impaired muscle performance. The intake of cocoa polyphenols has been suggested to improve muscle recovery due to their antioxidant and anti-inflammatory capacity. However, their bioavailability presents a challenge. Therefore, food microencapsulation may be an alternative to protect polyphenols, ensuring their biological effects. This study aimed to investigate the effect of a single dose of microencapsulated cocoa on the changes in muscle damage markers after eccentric exercise. In this randomized, double-blind, crossover study, fourteen healthy volunteers with previous resistance training experience performed 6 × 10 maximal isokinetic eccentric contractions of their elbow flexors using an isokinetic dynamometer after ingesting 25 g of microencapsulated cocoa or placebo. Peak isometric torque was measured using maximal voluntary isometric contractions, and pain was measured using a visual analogic scale both before and 24 h, 48 h, and 72 h after the damage protocol. Plasma glutathione and malondialdehyde levels were measured using high-performance liquid chromatography, and concentrations of myoglobin and C-reactive protein were determined using a fluorescence immunoassay analyzer. Significant decreases were seen in the peak isometric torque and pain measures from pre- to 72 h post-eccentric exercise. A significant main effect for time was found only for plasma myoglobin at 2 h, 48 h, and 72 h, and for C-reactive protein at 2 h, compared to the pre-eccentric exercise values. No significant time-treatment effects were observed (all p > 0.05). This study demonstrated that microencapsulated cocoa cannot improve muscle recovery after eccentric exercise, at least when a single dose is consumed.
]]>Applied Biosciences doi: 10.3390/applbiosci2040042
Authors: Janan Arslan Kurt Benke
Exploratory data analysis and statistical moments were used to investigate the potential impact of ceiling and floor effects in medical trials. A total of 150 treatment-naive eyes were assessed in a retrospective case study of patients who were treated with anti-VEGF injections for wet age-related macular degeneration. The experimental results revealed that ceiling and floor effects are problematic in data analysis and may result in serious errors when using standard parametric tests. The case study provided insights relating to methodology in medical trials, experimental data analysis, and statistical inference, as applied to the interpretation of treatment response limits. Suggestions are provided for statistical data pre-processing and post-processing when significantly skewed distributions are present in response groups.
]]>Applied Biosciences doi: 10.3390/applbiosci2040041
Authors: Philip A. Sapp Jeremy R. Townsend Trevor O. Kirby Marlies Govaert Cindy Duysburgh Massimo Marzorati Tess M. Marshall Ralph Esposito
While traditional multivitamin and mineral (MVM) supplements generally come in tablet form, new powder forms of MVM supplements are available with theoretically higher bioavailability relative to tablet MVM supplements. The purpose of this study was to assess the bioaccessibility and bioavailability of minerals (magnesium (Mg), zinc (Zn), calcium (Ca), and potassium (K)) in a tablet MVM supplement compared to a novel powder Foundational Nutrition supplement (AG1®), containing minerals, vitamins, phytochemicals, and pre-/probiotics, in the upper gastrointestinal tract. The tablet MVM supplement was specifically formulated for this study, with matched mineral contents and identical chemical structures. The adapted Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) model was used to assess the bioaccessibility and bioavailability of soluble minerals using a simulated upper gastrointestinal tract and dialysis membrane to mimic human digestion and absorption. The bioaccessibility was assessed at the end of the stomach and duodenum. The bioaccessibility and bioavailability were assessed at 1, 2, and 3 h following dialysis. The preliminary soluble mineral analysis of the tablet (crushed to a powder) and AG1 powder demonstrated significantly higher (p < 0.05) soluble fractions of Zn and Ca, but lower Mg in the AG1 powder vs. the tablet. The total soluble mineral percentages at the stomach and duodenum end were all significantly higher for the AG1 powder vs. the tablet (p < 0.05). Mg, Ca, and Zn were more (p < 0.05) bioaccessible and bioavailable in the powder compared to the tablet during the small intestine simulation. The bioaccessible fraction of K was higher (p < 0.05) only at 3 h for the tablet vs. the powder. These preclinical data demonstrate that the AG1 powder has superior dissolution and disintegration characteristics compared to the tablet, leading to increased bioaccessibility and bioavailability in vitro.
]]>Applied Biosciences doi: 10.3390/applbiosci2040040
Authors: Leonardo A. Linhares Carlos H. I. Ramos
Circular dichroism (CD) spectroscopy has emerged as a powerful tool in the study of protein folding, structure, and function. This review explores the versatile applications of CD spectroscopy in unraveling the intricate relationship between protein conformation and biological activity. A key advantage of CD spectroscopy is its ability to analyze protein samples with minimal quantity requirements, making it an attractive technique for studying proteins that are scarce or difficult to produce. Moreover, CD spectroscopy enables the monitoring of physical and chemical environmental effects on protein structures, providing valuable insights into the dynamic behavior of proteins in different conditions. In recent years, the use of synchrotron radiation as a light source for CD measurements has gained traction, offering enhanced sensitivity and resolution. By combining the advantages of CD spectroscopy, such as minimal sample requirements and the ability to probe environmental effects, with the emerging capabilities of synchrotron radiation (SRCD), researchers have an unprecedented opportunity to explore the diverse aspects of protein behavior. This review highlights the significance of CD spectroscopy in protein research and the growing role of synchrotron radiation in advancing our understanding of protein behavior, aiming to provide novel insights and applications in various fields, including drug discovery, protein engineering, and biotechnology. A brief overview of Solid-State Circular Dichroism (SSCD) is also included.
]]>Applied Biosciences doi: 10.3390/applbiosci2040039
Authors: Neelam Iqbal Tejal Pant Nanda Rohra Abhishek Goyal Merin Lawrence Anomitra Dey Payal Ganguly
Bone regeneration and repair are complex processes with the potential of added complications, like delayed repair, fracture non-union, and post-surgical infections. These conditions remain a challenge globally, pressurizing the economy and patients suffering from these conditions. Applications of nanotechnology (NBT) in the field of medicine have provided a medium for several approaches to support these global challenges. Tissue engineering is one such field that has been on the rise in the last three decades through the utilization of NBT for addressing the challenges related to bone regeneration. First, NBT enables the formation of scaffolds at the nanoscale needed for bone tissue engineering (BTE) using natural and synthetic polymers, as well as with minerals and metals. Then, it aids the development of the nano-formulation strategized to deliver antimicrobial drugs and/or growth factors through various ways to enhance bone repair through the scaffold. Third, NBT facilitates the use of specialized nanoparticles to image and track cellular events in vitro as well as in vivo. This review is an effort to bring together the current knowledge in the field of BTE and present the scope of ever-evolving NBT, a contribution towards precision medicine.
]]>Applied Biosciences doi: 10.3390/applbiosci2040038
Authors: Charbel A. Basset Inaya Hajj Hussein Abdo R. Jurjus Francesco Cappello Everly Conway de Macario Alberto J. L. Macario Angelo Leone
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.
]]>Applied Biosciences doi: 10.3390/applbiosci2040037
Authors: Sally A. Bound
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.
]]>Applied Biosciences doi: 10.3390/applbiosci2040036
Authors: Roger D. Lawrie Steven E. Massey
Single Nucleotide Polymorphisms (SNPs) are variations that occur at single nucleotides in the genome and are present at an appreciable level in a population. SNPs can be linked to phenotypes of interest, for example diseases, recent adaptations, or species hybridization. They can also be used to study phylogeny and evolutionary history. Technologies that rapidly identify and catalog the presence of SNPs in a DNA sample are known as SNP genotyping panels, and they continue to undergo rapid development. Such methods have great utility across the agricultural sciences in diverse areas such as plant and animal breeding, pathogen and pesticide resistance identification, outbreak tracing, and hybridization detection. Here, we provide an overview of 14 different SNP genotyping technologies and weigh some of the pros and cons associated with each platform. This review is not comprehensive or technical, nor does it aim to be. Rather, the objective is to provide an introduction to the landscape of genotyping technologies for researchers who do not have experience with these methods. Three classes of SNP genotyping methods are Polymerase Chain Reaction (PCR)-based (nine different methods), microarray-based (one method), and Next-Generation Sequencing (NGS)-based (four different methods). We discuss how each genotyping class is suited for different niches; PCR-based has a low SNP count and high sample number, microarray-based has a very high SNP count and a moderate sample number, and Next-Generation Sequencing-based has a moderate SNP count and moderate number of samples. Included are basics about how the methods function and example use cases of each method. Additionally, we introduce and discuss the potential for the MinION sequencer in SNP genotyping. For each technology, we provide insights into cost, equipment needs, labor costs, experimental complexity, data output complexity, and accessibility. These considerations address the feasibility of deploying the technologies in an agricultural science environment.
]]>Applied Biosciences doi: 10.3390/applbiosci2040035
Authors: Lauri H. Vaahtoniemi
Anterior tooth (ANT) contacts induce a short-latency reflex inhibition of the human jaw-closing muscles. The jaw is a rigid class 1 lever for pinpoint targeting muscle force into a single bite point, the pivoting food particle. Seesaw reflex movements around the food particle fulcrum multiply the food-crushing force. Unpredictable jolts of reaction force caused by food crushing are subjected to the rostral ANT and caudally to the two articulate ends of the jaw triangle. The compression/distraction strains of food crushing must be monitored and inhibited by withdrawal reflexes. The mesencephalic ganglion (Vmes), neural myelin sheath, and muscle stretch receptors evolved subsequently to the advent of jaws to improve the velocity of proprioceptive and withdrawal reflexes. In mammalians, the spindles of the taut motor units, stretched by the food fulcrum, send excitatory monosynaptic feedback for the efferent neurons of the respective ipsilateral muscle units via the Vmes. In the Vmes, the spindle-input-mediating afferent neurons are coupled with another source of afferent feedback, which is also excitatory, from the back tooth (BAT) mechanoreceptors. The two sources of excitatory pulses are summated and targeted for the efferent neurons to boost the stretched and taut motor units. Likewise, the afferent feedback from the ANT mechanoreceptors is also coupled in the Vmes with concomitant feedback from spindles. The ANT output, however, is inhibitory to negate the excitatory feedback from the stretched jaw muscle units. The inhibitory feed from the anterior teeth temporarily blocks the excitatory potential of the masticatory motor efferent neurons to protect the anterior teeth and jaw joints from inadvertent strains. The inhibitory inputs from the anterior teeth alternate with the excitatory inputs from the BAT to determine which jaw-closing muscle units are activated or inhibited at any given instant of food crushing. The Vmes exists in all jawed vertebrates, and its evolution was probably motivated by demands for the control of bite force. The monosynaptic unilateral food-crushing excitatory and inhibitory reflexes (UFCRs) override the coexisting bilaterally executed feed for the jaw muscles from the central nervous system. The hypothesis proposed in this study is that the Vmes-mediated UFCRs combine neural inputs from tooth contacts with concomitant feedback from the muscle stretch receptors for the control of the mammalian food-crushing bite force.
]]>Applied Biosciences doi: 10.3390/applbiosci2040034
Authors: Rahul Ravindran Kate S. Branigan Landon M. Lefebvre Blake T. Dotta
It has been previously reported that time-varying EMFs and LEDs have the potential to modulate cellular activity and cell viability. It has also been shown that cellular activity and state can be inferred by measuring the biophoton emission derived from these same cells. To identify if the brief application (15 min) of an LED (635 nm at 3 klx) or EMF (1–3 uT) could influence cell growth and subsequent biophoton emission characteristics, B16-BL6 cells were grown to confluence and exposed to a time-varying, frequency-modulated EMF, LED, or both. Before and after EMF and LED exposure, photon emission measurements were taken for 1 min at a 50 Hz sampling rate. Following the exposure and photon emission measurements, cell viability was assessed via the use of a hemocytometer. The results demonstrated that after only 15 min of exposure to a time-varying EMF, there was a 41.6% reduction in viable cells when compared to sham controls [t(25) = 2.4, p = 0.02]. This effect approached significance in the LED alone condition [p = 0.07] but was completely absent in the condition wherein the LED and EMF were applied simultaneously [p < 0.8]. Additionally, following exposure to only the LED, there was a significant increase in biophoton emission SPD values at 13 Hz from whole cell cultures [t(60) = 2.3, p = 0.021]. This biophoton emission frequency was also strongly correlated with the number of nonviable cells [r = −0.514] in the dish. Taken together, these data point to biophotons emitted from cell cultures at 13 Hz as a potential indicator of the number of nonviable cells in vitro. The summation of data here corroborates previous work demonstrating the efficacy of specific time-varying EMFs as a novel therapeutic for the inhibition of cancer cell growth. It also furthers our assertion that biophoton emission can be used as a novel detection tool for cell activity.
]]>Applied Biosciences doi: 10.3390/applbiosci2040033
Authors: Helna M. Baby John Joseph Maneesha K. Suresh Raja Biswas Deepthy Menon
An imperative requisite of tissue-engineered scaffolds is to promote host cell regeneration and concomitantly thwart microbial growth. Antibacterial agents are often added to prevent implant-related infections, which, however, aggravates the risk of bacterial resistance. For the first time, we report a fiber-based platform that selectively promotes the growth of mammalian cells and alleviates bacteria by varying fiber size, orientation, and material of polymeric yarns. The interactions of Gram-positive and -negative bacterial species with mammalian mesenchymal stem cells (MSC) were investigated on poly-€-caprolactone (PCL) yarns, polyethylene terephthalate (PET), poly-L-lactic acid (PLLA), and cotton. Various yarn configurations were studied by altering the fiber diameter (from nano- to microscale) and fiber orientations (aligned, twisted, and random) of PCL yarns. PCL nanofibrous yarn decreased the adhesion of S. aureus and E. coli, with a 2.7-fold and 1.5-fold reduction, respectively, compared to PCL microfibrous yarn. Among different fiber orientations, nanoaligned fibers resulted in an 8-fold and 30-fold reduction of S. aureus and E. coli adhesion compared to random fibers. Moreover, aligned orientation was superior in retarding the S. aureus adhesion by 14-fold compared to nanotwisted fibers. Our data demonstrate that polymeric yarns comprising fibers with nanoscale features and aligned orientation promote mammalian cell adhesion and spreading and concomitantly mitigate bacterial interaction. Moreover, we unveil the wicking of cells through polymeric yarns, facilitating early cell adhesion in fibrous scaffolds. Overall, this study provides insight to engineer scaffolds that couple superior interaction of mammalian cells with high-strength fibrous yarns for regenerative applications devoid of antibacterial agents or other surface modification strategies.
]]>Applied Biosciences doi: 10.3390/applbiosci2030032
Authors: Filippo Savini Natalie Mutter Katja Baumgartner Ivan Barišić
Bacterial contamination of water and food sources is still a major source of diseases. Early detection of potential pathogens is key to prevent their spreading and severe health risks. Here, we describe a fast, low-cost detection assay based on horseradish peroxidase (HRP) conjugated to streptavidin for the direct identification of bacteria. Streptavidin can bind to bacterial cells due to its high affinity for biotin, a natural component of microbial cell surfaces. Upon binding to bacteria, the HRP converts a chromogenic substrate, resulting in a visible color change. In the present study, we evaluated different detection platforms regarding their compatibility with the detection principle. To reduce background signals and increase the sensitivity of HRP-based assays, the binding of HRP to surfaces and biomolecules was intensively investigated. The final assay successfully detected the most relevant bacterial strains in drinking water, such as Escherichia coli, Klebsiella pneumonia, and Enterobacter cloacae.
]]>Applied Biosciences doi: 10.3390/applbiosci2030031
Authors: Ollo Youl Belinda Ramata Hafouo Moné-Bassavé Sibidou Yougbaré Boubacar Yaro Tata Kadiatou Traoré Rainatou Boly Josias B. Gérard Yaméogo Moumouni Koala Noufou Ouedraogo Elie Kabré Halidou Tinto Maminata Traoré-Coulibaly Adama Hilou
Dermatoses are essentially caused by infection or free radical aggression, immunoallergic disorders, or can be secondary to general diseases. Management of dermatoses by modern medicine is complex and costly, and the development of alternative treatments is urgent. Opilia amentacea Roxb. is a woody climber plant traditionally used in Burkina Faso for treatment of bad skin diseases. This study was carried out to evaluate the antimicrobial and antioxidant activities of extracts of O. amentacea and to characterize potent fractions. The antimicrobial activity was determined using the disc diffusion and microdilution methods, while antioxidant activity was assessed using the 2,2′-diphenyl-1-picrylhydrazyl radical (DPPH), 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) diammonium salt (ABTS) and ferric reducing antioxidant power (FRAP) assays. The content of the plant extracts in polyphenols and flavonoids was also studied. The results revealed several secondary metabolites in the leaves, stems and root bark extracts of the plant, including sterols, triterpenes, and flavonoids and tannins, and a generally high total polyphenol and total flavonoid content. Dichloromethane fractions of leaves (FDFe) and stem barks (FDET) exhibited the best antioxidant activity and were the most active on Gram-positive bacilli. Hexane leaves (FHFe) and hexane root bark (FHER) fractions exhibited the best antifungal activity against Candida tropicalis. High correlation (R2 = 0.932) was found between the total flavonoid content of extracts and ferric-reducing antioxidant power. In view of these results, the present study describes O. amentacea as a potential source of antibacterial, antifungal and antioxidant agents and justifies the traditional uses of the plant as an anti-dermatosis plant.
]]>Applied Biosciences doi: 10.3390/applbiosci2030030
Authors: Srinivas Sura Chamali Kodikara Surya Acharya Ali Sabra Champa Wijekoon
The interest in under-utilized crops as a functional food for animals and humans has been increasing recently with advancing research and the need for crop improvement. Canadian forage crops including alfalfa (Medicago sativa L.) and fenugreek (Trigonella foenum-graecum L.) are marketed in various forms due to their traditionally known health benefits. Sainfoin (Onobrychis viciifolia Scop.) is another forage crop with potential health benefits containing beneficial nutraceuticals. In this study, we assessed selected bioactive phenolic compounds and fatty acids in seeds and seedlings of Canadian-grown alfalfa, sainfoin, and fenugreek. Various phenolic compounds were detected in all three forage crop seeds and seedlings. In general, Sainfoin seeds were high in phenolic compounds relative to that of alfalfa and fenugreek. Chlorogenic acid, epigallo catechin, and gallic acid were at high concentrations at 56.6, 86.8, and 64.7 µg.g−1, respectively, compared to other phenolic compounds in sainfoin seeds. The fatty acids content (%) was significantly affected by the seedling stage and crop type. Some of the bioactive compounds present in seeds were not detected in seedling stages. The comparative bioactive phenolic compounds and fatty acid assessments of these forage legumes could potentially be used as biomarkers for the selection and development of favorable cultivars for animal and human nutrition. In addition, these crops could be used for isolating these bioactive compounds, and thus increasing their agri-food value.
]]>Applied Biosciences doi: 10.3390/applbiosci2030029
Authors: Martina Muste Sadurni Marco Saponaro
Deregulated transcription is a well-known characteristic of cancer cells, with differentially expressed genes being a common feature of several cancers. Often, deregulated transcription is a consequence of alterations in transcription factors (TFs), which play a crucial role in gene expression and can act as tumour suppressors or proto-oncogenes. In eukaryotic organisms, transcription is carried out by three distinct RNA polymerase complexes: Pol I, Pol II, and Pol III. Pol II, specifically, is responsible for transcribing messenger RNA (mRNA), the protein coding part of the genome, as well as long non-coding RNAs (lncRNAs). While there is considerable research on the impact of specific deregulated transcription factors in cancer development, there is a lack of studies focusing on defects within the RNA polymerase complexes and their subunits. This review aims to shed light in particular on the Pol II complex and highlight the deregulation of its subunits that have a significant impact on tumour development, prognosis, and survival. By providing a comprehensive overview of our current understanding of Pol II subunits in cancer, this review emphasizes the importance of further research in this area. It suggests that exploring these subunits’ deregulations could lead to the identification of valuable biomarkers and potential therapeutic targets, making it a topic of collective interest.
]]>Applied Biosciences doi: 10.3390/applbiosci2030028
Authors: Yunseol Park Jeesu Lee Hyunjin Shim
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.
]]>Applied Biosciences doi: 10.3390/applbiosci2030027
Authors: Ivanna Kramer Sabine Bauer
As schools go digital, the use of tablet computers is increasing. Concerns are raised that the extensive use of tablets and the associated bent-over posture may negatively affect the individual’s health. In order to analyse the possible effects of prolonged tablet use on physical health, a detailed analysis of the posture during tablet use is needed so that appropriate preventive measures can be taken to prevent degenerative changes. Therefore, the aim of this study was to measure and report the posture of 56 students while working with a tablet computer and compare it with an upright posture. Sagittal and frontal images were used for measurements of the subjects’ postures while seated, using the tablet, and in a neutral sitting position looking straight ahead. The body position during tablet use was recorded in two different user configurations: tablet flat on the table and tablet in individual freely chosen user configuration. After appropriate annotation of the data, the following parameters were evaluated in different planes. The craniovertebral angle (CVA), head tilt angle (HTA), and forward shoulder angle (FSA) are measurements that describe the extent to which the head bends forward and downward and how the shoulders are aligned in the sagittal plane. On the other hand, the head shoulder angle (HSA), lateral head tilt angle (LHTA), and trunk flexion angle (TFA) are angles measured in the frontal plane, which indicate the degree of head tilt and trunk bending to the right or left side. The measurement results clearly showed that the use of a tablet had a pronounced effect on the positions and rotations of the participants’ head, neck, and shoulders. This was evident through strong deviations observed in the angles measured between the sitting straight posture and the postures while using the tablet. For example, depending on the body posture class, the mean CVA values were 45.76° for straight sitting posture, 28.25° for holding the tablet individually posture, and 26.04° for the posture adopted while using a tablet placed flat on the table.
]]>Applied Biosciences doi: 10.3390/applbiosci2030026
Authors: Elizabeth R. Elliott Alaina C. Taul Maya O. Abul-Khoudoud Nicole Hensley Robin L. Cooper
Two-P-domain K+ (K2p) channels are responsible for maintaining the resting membrane potential. K2p channels have varied expression in healthy tissue, but they also change in cancerous or diseased states. The correlation and causation as regards the alteration of K2p channel expression are still being investigated. The compound doxapram seems to block K2p channels and depolarize cells. Using Drosophila, the increased expression of the ORK1 K2p channel in cardiac and skeletal muscle was investigated. The heart rate in larval Drosophila is very sensitive to pH, and since doxapram blocks a subset of the K2p channels that are known to be acid-sensitive, it was postulated that doxapram would affect heart rate. A pH change from 7.1 to 6.5 increased the rate, while that from 7.1 to 7.5 decreased the rate. An amount of 0.1 mM of doxapram had no effect, but 0.5 of mM depressed Drosophila heart rates within five minutes. Exposure to 5 mM of doxapram immediately decreased the rate. Lipopolysaccharides (LPSs) from Gram-negative bacteria acutely increased the rate. LPSs activate K2p channels in the skeletal muscle of larvae and are blocked by doxapram. LPSs slightly reduce depression in the rate induced by doxapram. The overexpression of K2p channels in the heart and skeletal muscle depressed the heart rate and heightened pH sensitivity. At larval neuromuscular junctions, the overexpression in skeletal muscle increases the frequency of spontaneous quantal events and produces a more negative resting membrane potential.
]]>Applied Biosciences doi: 10.3390/applbiosci2030025
Authors: Janan Arslan Kurt Benke
The build-up of lipofuscin—an age-associated biomarker referred to as hyperfluorescence—is considered a precursor in the progression of geographic atrophy (GA). Prior studies have attempted to classify hyperfluorescent regions to explain varying rates of GA progression. In this study, digital image processing and unsupervised learning were used to (1) completely automate the extraction of hyperfluorescent regions from images, and (2) evaluate prospective patterns and groupings of hyperfluorescent areas associated with varying levels of GA progression. Patterns were determined by clustering methods, such as k-Means, and performance was evaluated using metrics such as the Silhouette Coefficient (SC), the Davies–Bouldin Index (DBI), and the Calinski–Harabasz Index (CHI). Automated extraction of hyperfluorescent regions was carried out using pseudocoloring techniques. The approach revealed three distinct types of hyperfluorescence based on color intensity changes: early-stage hyperfluorescence, intermediate-stage hyperfluorescence, and late-stage hyperfluorescence, with the early and late stages having three additional subclassifications that could explain varying levels of GA progression. The performance metrics for early-stage hyperfluorescence were SC = 0.597, DBI = 0.915, and CHI = 186.989. For late-stage hyperfluorescence, SC = 0.593, DBI = 1.013, and CHI = 217.325. No meaningful subclusters were identified for the intermediate-stage hyperfluorescence, possibly because it is a transitional phase of hyperfluorescence progression.
]]>Applied Biosciences doi: 10.3390/applbiosci2030024
Authors: John Irwin Edwin Bingham
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.
]]>Applied Biosciences doi: 10.3390/applbiosci2030023
Authors: Maria Inês Rouxinol Maria Rosário Martins João Mota Barroso Ana Elisa Rato
Red wine grapes have an important impact on the economy of many regions, both for wine quality and for their richness in phenolic compounds, which have many health benefits. Climate has been changing substantially in the last years, which affects greatly grape polyphenolic composition and wine quality. In this review, we will unveil the importance of climate in grape development, both physically and chemically, the different methodologies used to evaluate grape quality, the interesting new approaches using NIR spectroscopy, and the functional properties of grapes and red wine, due to their high phenolic content. Climate has an impact in the development of phenolic compounds in grapes, namely in the anthocyanins biosynthesis. The phenolic chemical composition changes during maturation, therefore, it is essential to keep on track the accumulation of these key compounds. This information is crucial to help producers choose the best harvest date since specific compounds like polyphenols are responsible for the color, taste, and mouthfeel of wines, which directly affects wine quality. The usage of different methodologies to assess quality parameters in grapes and wine, can be used to provide essential information to create the chemical profile of each variety to develop calibration methods. NIR spectroscopy seems to be a reliable method to be used in vineyards during grape maturation to provide real time information on quality parameters to producers since many reliable calibration models have been developed over time.
]]>Applied Biosciences doi: 10.3390/applbiosci2030022
Authors: Durga P. M. Chinthalapudi Sapna Pokhrel William L. Kingery Mark W. Shankle Shankar Ganapathi Shanmugam
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.
]]>Applied Biosciences doi: 10.3390/applbiosci2020021
Authors: Giancarlo A. Cuadra Abrar Shamim Raivat Shah Joey Morgan Dominic L. Palazzolo
Background: Expansion of OKF6/TERT-2 oral epithelial cells in vitro is important for studying the molecular biology of disease and pathology affecting the oral cavity. Keratinocyte serum-free medium (KSFM) is the medium of choice for this cell line. This study compares three media for OKF6/TERT-2 cultures: KSFM, Dulbecco’s Modified Eagle Medium/Nutrient Mixture of Hams F-12 (DMEM/F12), and a composite medium comprised of DMEM/F-12 and KSFM (1:1 v/v), referred to as DFK. The toxicological effects of electronic cigarette liquids (e-liquids) on OKF6/TERT-2 cells cultured in these media were also compared. Methods: Cells were cultured in KSFM, DMEM/F12, or DFK, and cellular morphology, growth, wound healing and the gene expression of mucins and tight junctions were evaluated. Additionally, cytotoxicity was determined after e-liquid exposures. Results: Switching from KSFM to DMEM/F12 or DFK 24 h post-seeding leads to typical cellular morphologies, and these cultures reach confluency faster than those in KSFM. Wound-healing recovery occurred fastest in DFK. Except for claudin-1, there is no difference in expression of the other genes tested. Additionally, e-liquid cytotoxicity appears to be amplified in DFK cultures. Conclusions: DMEM/F12 and DFK are alternative media for OKF6/TERT-2 cell culture to study the molecular biology of disease and pathology, provided cells are initially seeded in KSFM.
]]>Applied Biosciences doi: 10.3390/applbiosci2020020
Authors: Thomas Krause Mike Zickfeld Sebastian Bruchhaus Thoralf Reis Marco X. Bornschlegl Paolo Buono Michael Kramer Paul Mc Kevitt Matthias Hemmje
Genomics-based diagnostic data (GBDD) are becoming increasingly important for laboratory diagnostics. Due to the large quantity of data and their heterogeneity, GBDD poses a big data challenge. Current analysis tools for GBDD are primarily designed for research and do not meet the requirements of laboratory diagnostics for automation, reliability, transparency, reproducibility, robustness, and accessibility. This makes it difficult for laboratories to use these tools in tests that need to be validated according to regulatory frameworks and to execute tests in a time- and cost-efficient manner. In order to better address these requirements, we propose an event-driven workflow-based architecture as the basis for a processing platform that is highly scalable using container technologies and microservices. A prototype implementation of this approach, called GenomicInsights, has been developed and evaluated to demonstrate its feasibility and suitability for laboratory diagnostics.
]]>Applied Biosciences doi: 10.3390/applbiosci2020019
Authors: Benedikt Hülsemann Marian Baumgart Leonhard Lenz Elviliana Marie Föllmer Gregor Sailer Konstantin Dinkler Hans Oechsner
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.
]]>Applied Biosciences doi: 10.3390/applbiosci2020018
Authors: Foteini K. Kozaniti Aikaterini E. Manara Vassilis Kostopoulos Panagiotis Mallis Efstathios Michalopoulos Demosthenes Polyzos Despina D. Deligianni Diana V. Portan
Computational methods were combined with an experimental setup in order to investigate the response of human umbilical cord stem cells to 3D electrospun and printed scaffolds, when dynamically stimulated in a bioreactor. Key parameters associated to bioreactor working conditions were computationally investigated using Comsol software to use the output for the planned experimental setup. Based on the theoretical observations, the influence of the inlet velocity, cell number, and exposure time in the bioreactor were analyzed and the in vitro parameters were adjusted accordingly. MSCs were seeded in different numbers in the 3D porous scaffolds and stimulated in the bioreactor (0.5 and 2 h duration, 3 and 6 mm/s inlet velocity). Polycaprolactone 3D electrospun, and polyurethane and polylactic acid 3D-printed scaffolds were fabricated and fibronectin-coated. The computational study predicted initial events in the process of cells deposition and attachment. Total protein, osteopontin, and osteocalcin levels in cells deposited in scaffolds were investigated; SEM and confocal imaging confirmed the biomarker analysis. MSCs proliferated well in PCL. Polyurethane enabled extremely rapid proliferation followed by differentiation, while PLA induced a moderate proliferation and parallel mineralization. The scaffolds stiffness has been found as the key enabling parameter decisive for cells feedback.
]]>Applied Biosciences doi: 10.3390/applbiosci2020017
Authors: Nicole Hensley Elizabeth R. Elliott Maya O. Abul-Khoudoud Robin L. Cooper
Cardiac contractile cells depend on calcium in order to function. Understanding the regulation of calcium influx, efflux, and release from the sarcoplasmic reticulum is essential. The focus of this investigation is to address how a reduction of functional Ca2+-activated K+ (KCa) channels, via a mutational line, might impact the heart rate in larva when the SER is also modulated through Ca2+ loading and stimulation. The larval heart tube is exposed in situ and flushed with saline. With a known saline composition, a potential therapeutic pharmacological agent, 2-Aminoethyl diphenylborinate (2-APB), was examined for its effect on heart rate, as well as to determine the contribution from KCa channels. In this study, it was determined that mutation in the K(Ca) channel (i.e., Slo) showed a different trend than the wild-type CS strain. Exposure to high concentrations of 50 µM 2-APB decreased heart rate in the Slo strain and increased it in the wild-type CS strain. Serotonin increased heart rate in both thapsigargin- and 2-APB-treated larvae, with no significant difference between the strains.
]]>Applied Biosciences doi: 10.3390/applbiosci2020016
Authors: Fernanda Caro Beveridge Alwyn Williams Robyn Cave Sundaravelpandian Kalaipandian Steve W. Adkins
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.
]]>Applied Biosciences doi: 10.3390/applbiosci2020015
Authors: Chrysanthi Zarmakoupi Konstantinos Mpistiolis George Pantazis Panagiota Psatha Despoina Dimitriadi Foteini Kitsiou Panagiotis Eliopoulos George Patakioutas Spiridon Mantzoukas
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.
]]>Applied Biosciences doi: 10.3390/applbiosci2020014
Authors: Tamara Martin-Pozas Jose Luis Gonzalez-Pimentel Valme Jurado Leonila Laiz Juan Carlos Cañaveras Angel Fernandez-Cortes Soledad Cuezva Sergio Sanchez-Moral Cesareo Saiz-Jimenez
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.
]]>Applied Biosciences doi: 10.3390/applbiosci2020013
Authors: Isabel Gameiro-Ros Lelia Noble Ming Tong Emine B. Yalcin Suzanne M. de la Monte
Central nervous system (CNS) white matter pathologies accompany many diseases across the lifespan, yet their biochemical bases, mechanisms, and consequences have remained poorly understood due to the complexity of myelin lipid-based research. However, recent advances in matrix-assisted laser desorption/ionization-imaging mass spectrometry (MALDI-IMS) have minimized or eliminated many technical challenges that previously limited progress in CNS disease-based lipidomic research. MALDI-IMS can be used for lipid identification, semi-quantification, and the refined interpretation of histopathology. The present work illustrates the use of tissue micro-arrays (TMAs) for MALDI-IMS analysis of frontal lobe white matter biochemical lipidomic pathology in an experimental rat model of chronic ethanol feeding. The use of TMAs combines workload efficiency with the robustness and uniformity of data acquisition. The methods described for generating TMAs enable simultaneous comparisons of lipid profiles across multiple samples under identical conditions. With the methods described, we demonstrate significant reductions in phosphatidylinositol and increases in phosphatidylcholine in the frontal white matter of chronic ethanol-fed rats. Together with the use of a novel rapid peak alignment protocol, this approach facilitates reliable inter- and intra-group comparisons of MALDI-IMS data from experimental models and could be extended to human disease states, including using archival specimens.
]]>Applied Biosciences doi: 10.3390/applbiosci2020012
Authors: Stefano Burgio Olga Maria Manna Giorgia Intili Francesco Cappello Fabio Bucchieri
Over the last ten years, with the progress of in vitro culture methods, it has been possible to build increasingly reliable models to effectively mimic in vivo ones. The translational methodological approach that combined biotechnology and biomedical engineering has produced remarkable results, such as the development of ex vivo 3D culture models, the construction of on-a-chip organoids, and the construction of complex systems capable of bypassing the static nature of the two-dimensional cultural models that have been typical of in vitro studies conducted to date. However, nowadays, there is still reluctance to completely abandon the animal model as an essential reference or as an integrated step for the validation of a model or a proposed study. This is due to the partially correct conviction of the impossibility of reproducing, in vitro or ex vivo, the complexity of pathological models or the spatial communication between different cytotypes, as well as, more generally, the lack of systems capable of mimicking the dynamism of a complex in vivo system. In this study, we will compare different methodological approaches in the study of the three most common types of respiratory diseases: chronic obstructive pulmonary disease (COPD), asthma, and lung carcinomas. The purpose of this comparative study is to evaluate the most current methodological approaches to understand how far research is from being independent from animal models. Animal studies are generally considered necessary, but are still questioned because of the ethics and the cost–benefit ratio involved.
]]>Applied Biosciences doi: 10.3390/applbiosci2020011
Authors: Noel Gahamanyi Therese Umuhoza Shamsaldeen Ibrahim Saeed Landry Ndriko Mayigane Jean Nepomuscene Hakizimana
Antimicrobial resistance (AMR) is one of the top 10 global health threats facing humanity, and the sub-Saharan Africa (SSA) is among the heavily affected regions due to its weak health systems and limited resources. Due to an escalating number of AMR pathogens and the scarcity of new antimicrobials, efforts in the prevention of infections and the search for alternative treatment options are ongoing. The objective of this review was to assess important weapons against AMR in SSA. The highlighted weapons include vaccines, education and awareness, infection prevention and control (IPC) using water, sanitation, and hygiene (WASH), alternative treatment options, the One Health (OH) approach, AMR surveillance, operational national action plans (NAPs) on AMR, antimicrobial stewardship (AMS) programs, and good governance and regulations. Despite not being used at a satisfactory level in SSA, advanced techniques in dealing with AMR in SSA include (i) metagenomics, (ii) whole-genome sequencing (WGS) in AMR surveillance to track resistance trends and know when to intervene, and (iii) use of artificial intelligence in AMR prediction based on genomics data. The fight against AMR threat in SSA has embraced a number of currently available strategies, and developing new ones will lower the consequences of such a threat for future generations.
]]>Applied Biosciences doi: 10.3390/applbiosci2010010
Authors: Vincent Chaplot Isack Mathew Alistair Clulow Hussein Shimelis
The transfer of atmospheric carbon (C) in soils is a possible strategy for climate change mitigation and for restoring land productivity. While some studies have compared the ability of existing crops to allocate C into the soil, the genetic variations between crop genotypes have received less attention. The objective of this study was to compare the allocation to the soil of atmospheric C by genetically diverse wheat genotypes under different scenarios of soil water availability. The experiments were set up under open-field and greenhouse conditions with 100 wheat genotypes sourced from the International Maize and Wheat Improvement Centre and grown at 25% (drought stressed) and 75% (non-stressed) field capacity, using an alpha lattice design with 10 incomplete blocks and 10 genotypes per block. The genotypes were analyzed for grain yield (GY), plant shoot and root biomass (SB and RB, respectively) and C content, and stocks in plant parts. Additionally, 13C pulse labeling was performed during the crop growth period of 10 selected genotypes for assessing soil C inputs. The average GY varied from 75 to 4696 g m−2 and total plant biomass (PB) from 1967 to 13,528 g m−2. The plant C stocks ranged from 592 to 1109 g C m−2 (i.e., an 87% difference) under drought condition and between 1324 and 2881 g C m−2 (i.e., 117%) under well-watered conditions. Atmospheric C transfer to the soil only occurred under well-drained conditions and increased with the increase in the root to shoot ratio for C stocks (r = 0.71). Interestingly, the highest transfer to the soil was found for LM-26 and LM-47 (13C/12C of 7.6 and 6.5 per mille, respectively) as compared to LM-70 and BW-162 (0.75; 0.85). More is to be done to estimate the differences in C fluxes to the soil over entire growing seasons and to assess the long-term stabilization of the newly allocated C. Future research studies also need to identify genomic regions associated with GY and soil C transfer to enable the breeding of “carbon-superior” cultivars.
]]>Applied Biosciences doi: 10.3390/applbiosci2010009
Authors: Marta I. Magalhães Ana P. C. Almeida
Multifunctional materials and devices with captivating properties can be assembled from cellulose and cellulose-based composite materials combining functionality with structural performance. Cellulose is one of the most abundant renewable materials with captivating properties, such as mechanical robustness, biocompatibility, and biodegradability. Cellulose is a low-cost and abundant biodegradable resource, CO2 neutral, with a wide variety of fibers available all over the world. Over thousands of years, nature has perfected cellulose-based materials according to their needs, such as function vs. structure. Mimicking molecular structures at the nano-, micro-, and macroscales existing in nature is a great strategy to produce synthetic cellulose-based active materials. A concise background of cellulose and its structural organization, as well as the nomenclature of cellulose nanomaterials, are first addressed. Key examples of nature-designed materials with unique characteristics, such as “eternal” coloration and water-induced movement are presented. The production of biomimetic fiber and 2D fiber-based cellulosic materials that have attracted significant attention within the scientific community are represented. Nature-inspired materials with a focus on functionality and response to an external stimulus are reported. Some examples of 3D-printed cellulosic materials bioinspired, reported recently in the literature, are addressed. Finally, printed cellulosic materials that morph from a 1D strand or 2D surface into a 3D shape, in response to an external stimulus, are reported. The purpose of this review is to discuss the most recent developments in the field of “nature-inspired” cellulose-based active materials regarding design, manufacturing, and inspirational sources that feature existing tendencies.
]]>Applied Biosciences doi: 10.3390/applbiosci2010008
Authors: Yousif Abdullah Abas Ayten Eroğlu Abdullah Dalar Musa Türker Fethi Ahmet Ozdemir Gaweł Sołowski
Chicory (Cichorium intybus L.) is a low-height perennial or biennial herb from the family of Asteraceae. Investigation of different in vitro regeneration strategies of Cichorium intybus and increasing the number of secondary metabolites in vitro regenerated plant samples were the aims of the research. Callus and plant regenerations were achieved in basal plant growth media supplemented with plant growth regulators (PGRs). Whole plant regeneration was carried out by direct organogenesis from leaf explant in Murashige and Skoog (MS) and B5 media supplemented with naphthalene acetic (NAA) acid and indole-3-butyric acid (IBA). The highest callus quantity was produced in MS medium supplemented with indole-3-acetic acid (IAA) and benzyl amino purine (BAP). The combination and concentrations of PGRs used in MS and B5 media not only provided root and shoot formation with callus, but also caused a change in the amounts of phenolic components. In addition, some PGRs used caused an increase in the number of phenolic compounds in callus and shoots developed from the leaf explant. When plants that grow in vitro and in vivo are compared with each other, it has been determined that plants grown in vivo contain higher amounts of some phenolic compounds. In vivo and in vitro samples were extracted in ethanol/water (80:20 v/v). The analysis of phenolic compounds (caftaric, chicoric, and chlorogenic acids and esculin) were performed in high-performance liquid chromatography (HPLC) and inulin was in UV spectrophotometry. The caftaric and chlorogenic acids and inulin concentrations were higher in vivo samples than that in vitro. Contrarily, esculin, and chicoric acid concentrations were higher in the in vitro regenerated samples. The higher concentration of valuable compounds in the in vitro regenerated samples, especially in callus tissue, gives hope for large-scale production of secondary metabolites under laboratory conditions.
]]>Applied Biosciences doi: 10.3390/applbiosci2010007
Authors: Xuchao Zhang Nadine Saul Thora Lieke Yi Chen Min Wu Bo Pan Christian E. W. Steinberg
As an effective soil amendment, biochars require a comprehensive ecological evaluation before they can be widely used in agriculture because endogenous contaminants, such as environmentally persistent free radicals (EPFRs), certainly pose an ecological risk to soil invertebrates. In this study, Caenorhabditis elegans (C. elegans) was used as a model organism to investigate the neurotoxicity of two rice straw biochars pyrolyzed at 500 and 700 °C. After 24 h exposure to unwashed biochar, washed biochar, and leaching fluids (supernatants), the neurobehavioral parameters of C. elegans were determined in a liquid toxicity test. The results showed that the washed 700 °C biochar particles significantly impaired locomotion and prolonged the defecation interval at a biochar concentration of 4 g·well−1, while the unwashed biochar and supernatants caused no apparent impairment. Supporting this, electron paramagnetic resonance (EPR) results showed that the intensity of EPFRs in unwashed 700 °C biochar was stronger than that of the corresponding washed particles. This indicates that, in the liquid test, the EPR signal alone is not indicative of particle toxicity. The accessibility and activity of the EPFRs should be considered. Dissolved organic matter (DOM) was observed in the leaching fluids. The neurotoxic activity of the washed biochar was alleviated after the re-addition of leaching fluids to the washed biochar, suggesting that the dissolved organic materials modulate the reactivity of the EPFRs in the liquid phase. This study suggests that the leaching process may increase the risk of biochar when used in the field environment.
]]>Applied Biosciences doi: 10.3390/applbiosci2010006
Authors: Gus R. McFarlane C. Bruce A. Whitelaw Simon G. Lillico
Scientists have long sought a technology to humanely control populations of damaging invasive pests in a species-specific manner. Gene drive technology could see this become a reality. This review charts the twists and turns on the road to developing gene drives in vertebrates. We focus on rodents, as these will likely be the first targets, and trace the journey from the early understanding of selfish genetic elements to engineering gene drives in mice; before discussing future research focuses and the crucial role that public perception and governance will play in the application of this technology. The realisation of robust gene drive strategies in vertebrate pests has the potential to revolutionise biocontrol.
]]>Applied Biosciences doi: 10.3390/applbiosci2010005
Authors: Isadora P. Siba Bruno J. Martynhak Marcela Pereira
The literature on the crosstalk between the brain and the gut has increased considerably in recent years. It is widely accepted now that the microbiome plays a significant role in several brain disorders, neurodevelopment, neurocognitive stages, and physiological functions. However, the mechanisms that influence such crosstalk are still not well elucidated. In this sense, one of the possible mechanisms by which the microbiome could influence brain function is through gut hormones released by enteroendocrine cells: ghrelin, cholecystokinin (CCK), peptide YY (PYY), vasoactive intestinal polypeptide (VIP), glucagon-like peptide (GLP1-2), corticotropin-releasing factor (CRF), glucose-dependent insulinotropic polypeptide (GIP), secretin, serotonin (5-HT), and oxytocin. Especially when one considers that the brain expresses receptors for these hormones in areas important to the neurobiology of brain disorders (e.g., depression), such as the hippocampus, amygdala, hypothalamus, and suprachiasmatic nucleus. To strengthen this hypothesis, gastrointestinal dysfunction (such as altered motility or pain) is relatively common in depressive patients, and changes in diet (low-carbohydrate diets, for example) positively affect mood. Additionally, alterations in the gut microbiome are relatively common in depressive patients and are related to the levels of Akkermansia, Lactobacillus, Bifidobacteria, Faecalibacterium, Roseburia and Clostridium. Finally, concerning the gut-released hormones, the literature reports that ghrelin can be a peripheral marker for the antidepressant treatment success rate and has elevated levels during depression. GLP-1 is tightly correlated with HPA axis activity being decreased by high cortisol levels. CCK seems to be altered in depression due to increased inflammation and activation of Toll-like receptor 4. Such finds allow the postulation that hormones, the microbiome and mood are intertwined and co-dependent. VIP is correlated with circadian rhythms. There is a bidirectional connection of the circadian rhythms between the host and the microbiota. Circadian rhythm disruption is associated with both poor outcomes in mental health and alterations in the microbiota composition. In sum, in the past year, more and more research has been published showing the tight connection between gut and brain health and trying to decipher the feedback in play. Here, we focus on depression.
]]>Applied Biosciences doi: 10.3390/applbiosci2010004
Authors: Hironaga Akita Yoshiki Shinto Zen-ichiro Kimura
Microbiologically influenced corrosion (MIC) of metal alloys is promoted by biofilms formed on metal surfaces. In the marine environment, MIC causes serious metal infrastructure problems, which lead to significant economic losses. In this study, we used an enrichment culture approach to examine the bacterial community that grows on metal surface at levels below the detection limit as a preliminary study for developing guidelines to prevent biofilm formation. An enrichment culture approach was employed to analyze the bacterial community on metal surface without biofilms and corrosion. Genomic DNA was extracted from culture sample after incubation in the enrichment culture with a metal piece, and then the V3–V4 variable regions of the bacterial 16S rRNA gene were amplified using the extracted genomic DNA as the template. Subsequently, using a next-generation sequencing approach, the amplified V3–V4 regions were sequenced, and the bacterial community was analyzed using the QIIME 2 microbiome bioinformatics platform. Using this enrichment culture approach, more than 80 bacterial genera were detected with Sphingomonas bacteria exhibiting the highest relative abundance (44%). These results demonstrated that this method could be useful for bacterial community analysis for bacteria below detection limits, and will serve as a basis for the development of the guidelines.
]]>Applied Biosciences doi: 10.3390/applbiosci2010003
Authors: Applied Biosciences Editorial Office Applied Biosciences Editorial Office
High-quality academic publishing is built on rigorous peer review [...]
]]>Applied Biosciences doi: 10.3390/applbiosci2010002
Authors: Angelica Naka Midori Kurahashi
Microalgae are a source of carbohydrates, proteins and lipids. Thus, they can be considered as raw material to transition from current fossil fuel-based refineries to biorefineries. Microalgae harvesting is considered a major challenge in biomass production. There are several harvesting techniques, but the majority of them are either expensive or not effective. The harvesting method that we propose is sedimentation-induced by light blockage, taking advantage of the motility characteristics of certain microalgae. In this research, the halophilic microalgae Dunaliella salina was selected. Experiments were conducted under light and dark conditions to compare the sedimentation rates. Sedimentation behavior was measured by collecting data on the optical density and cell count under both light and dark conditions. The results showed that, under light conditions, the cell count in the middle of the flask decreased from 1 × 106 cell/mL to 5 × 104 cell/mL after 50 days. Under dark conditions sedimentation took less than 10 days for complete settlement. Leaving Dunaliella salina under dark conditions may constitute a promising harvest method as this provides a high recovery rate and requires low energy.
]]>Applied Biosciences doi: 10.3390/applbiosci2010001
Authors: Thomas P. West
The ability of Aspergillus niger strains to support citric acid production using solid-state fermentation of agricultural processing coproducts was examined in this review. Citric acid has been shown to have a number of commercial applications in the food and beverage industries. The A. niger strains capable of elevated citric acid production are known to contain genetic mutations that stimulate overproduction of the organic acid likely involving citric acid cycle reactions. The agricultural processing coproducts previously examined for their ability to support citric acid production by A. niger solid-state fermentation include fruit processing wastes, sugarcane bagasse, starch vegetable processing wastes and cereal grain processing coproducts. A comparison of citric acid production by A. niger strains using solid-state fermentation demonstrated that certain agricultural processing coproducts were more effective in supporting a high level of acid synthesis. In particular, fruit processing wastes, such as apple pomace, banana peels, grape pomace and orange peels, supported high levels of citric acid by the fungal strains following solid-state fermentation. On the other hand, processing coproducts of cereal grains, such as brans and ethanol processing coproducts, supported low levels of citric acid production by the A. niger strains using solid-state fermentation. It appeared that the cereal processing coproducts provided less available sugar content to support citric acid production by the fungal strains. It was concluded that the level of citric acid produced by the A. niger strains during solid-state fermentation was dependent on the sugar content of the agricultural processing coproduct utilized.
]]>Applied Biosciences doi: 10.3390/applbiosci1030020
Authors: Carlton Ranjith Wilson Alphonse Rajesh Kannan Rajaretinam
The zebrafish model is an emerging model for the study of the complex behavioural patterns noted in depression and neurological disorders. Confinement and memory loss are linked with cognition and mental health impairment, where confinement paradigms are assessed using other behavioural responses based on novel tanks or T tanks. Since zebrafish are exploratory animals, the impact during confinement cannot be evaluated using a novel tank or T tank. The present study investigates the response of the zebrafish to acute confinement and assesses its memory-based learning behaviour through parameters such as movement, swimming speed, and time spent inside the confined space. The movement and swimming speed of the fishes in confinement showed no significant difference. When confined inside a space, the fish showed their anxiety with erratic movements or bouts of freezing, which declined by 83%, during the six days of confinement and the escape time from the confinement space also decreased by 58%. The impact of anxiety, resulting in clockwise and counter-clockwise movement, also reduced after three days. Our results summarise that the decrease in anxiety can help the fish in habituating itself to a forced condition. This experiment on zebrafish behavioural biology is used to assess the cognitive behaviour against confinement, and it emphasizes the learning of behavioural adaptions under both crowded and solitary conditions.
]]>Applied Biosciences doi: 10.3390/applbiosci1030019
Authors: Angélica Sinaí Quintanilla-Martínez Lizet Aguirre-Güitrón Luis Daniel Espinosa-Chaurand Mayra Diaz-Ramírez Alejandro De Jesús Cortés-Sánchez
Fish are marketed as a food and consumed worldwide. During the production of food, contamination by microorganisms is possible through the air, soil, water, surfaces, food handlers, etc. The air does not have a natural microbial composition, but it is a vehicle for the transmission of microorganisms of economic and health interest because they are associated with food spoilage and human diseases. The objective of this study was the microbiological analysis of the air in an area popular for the processing and marketing of fish products in the city of Tepic Nayarit. Using the passive or sedimentation method to collect microorganisms present in the air, the proportion of aerobic mesophile bacteria, coliform bacteria, fungi and yeast was determined at different locations in the fish processing and marketing area for four weeks. The results indicated that the aerobic mesophiles had the highest counts among all the microbial groups analyzed at the twelve different sampling points during the four weeks of the study; their numbers ranged from 2.44 to 2.95 log CFU/m3/h, followed by molds with counts from 1.44 to 2.75 log CFU/m3/h, yeasts with counts from 0.7 to 2.01 log CFU/m3/h and coliforms with counts that ranged from 0.7 to 1.68 log CFU/m3/h. We determined the proportion of the viable microbiological population present in the air at the different sampling points of the study area; several of these sampling points presented values above those recommended by various agencies around the world. Knowledge of the biological hazards transported through the air is important to establish and reduce the risk to the health of occupants and the contamination pathways of processed and marketed fishery products that may be associated with spoilage and foodborne diseases.
]]>Applied Biosciences doi: 10.3390/applbiosci1030018
Authors: Terrence J. Ravine Jonathan O. Rayner Rosemary W. Roberts James H. Davis Mohammad Soltani
Quaternary ammonium compounds (QACs) are routinely used as disinfectants in a variety of settings. They are generally effective against a wide range of microbes but often exhibit undesirable toxicity. Consequently, companies are constantly seeking alternatives to QACs that are just as effective but with reduced health and environmental hazards. Two boronium salt derivatives were tested against influenza A and SARS-CoV-2 viruses. One salt possessed a terminal benzyl group, while the other lacked the same terminal benzyl group. Both salts demonstrated virus inactivation similar to a commercial QAC disinfectant. The non-benzylated form exhibited the same cell toxicity profile as the QAC. However, the benzylated form displayed less cell toxicity than both the non-benzylated form and QAC. These results suggest that the boronium salts may be suitable for use as a disinfecting agent against enveloped viruses in lieu of using a QAC. Continued evaluation of the boronium salts is warranted to determine the lowest effective concentration capable of effectively controlling influenza A and SARS-CoV-2 viruses that also demonstrates low cytotoxicity.
]]>Applied Biosciences doi: 10.3390/applbiosci1030017
Authors: Chiemela S. Odoemelam Elena Hunter Daniela Eberl Baptiste Busi Zeeshan Ahmad Samuel White Philippe B. Wilson
Due to the aromatase enzyme’s involvement in estrogen biosynthesis, aromatase inhibitors have emerged as the preferred treatment for postmenopausal women with ER+ breast cancer. Using computational chemistry tools, we investigate how the human placental aromatase cytochrome P450 interacts with various phorbols with distinct chains at C-12, C-13, and C-20, as well as the well-known aromatase inhibitors anastrozole, exemestane, and letrozole. To identify phorbol-aromatase interactions, we performed a protein–ligand docking using the structures of our ligands and proteins using the Flare software (version 2.0, Cresset Software, Litlington, UK). These preliminary findings show that the phorbols considered (P-12,13-diAcPh, P-12,13-diiBu, P-12AcPh-13iBu, P-12Ang-13iBu, P-20Ac-12AcPh-13iBu and P-20Ac-12Ang-13iBu) had the highest binding energies in comparison with the commercially available aromatase inhibitors (anastrozole, letrozole, exemestane) used in this study. A subset of the previously described binding residues of testosterone (TST), the endogenous ligand, were also found to be responsible for the phorbol diesters’ binding to the aromatase enzyme, as demonstrated by the findings. This further suggests that the phorbol diesters can bind efficiently to CYP19A1 and may be able to alter its activity because they had higher binding energies than the commercially available drugs.
]]>Applied Biosciences doi: 10.3390/applbiosci1030016
Authors: Aref Abbasi Moud Aliyeh Abbasi Moud
Films made from cellulose nanocrystals (CNCs) may have iridescent structural colours (pure or in combination with other materials). Numerous fields might benefit from understanding how CNC self-assembly constructs these periodic structures. Herein, we looked at the colloidal characteristics of CNC particles as well as the development and behaviour of liquid crystals (LCs). We conducted a very brief literature analysis on the main issues related to the chiral structure creation of CNC LCs, including the origins of chirality, orientation, as well as its mechanical properties. Finally, by altering the pitch size, applications such as energy storage, humidity sensing, and photonic crystals were studied in a case-by-case manner. The manuscript, it is observed that the rational design of metamaterials built on CNCs allows for the reversible changing of colours through physical and chemical modifications by adding chemical or changing environmental factors. Examples of this alteration include the use of solvents, chemical penetration in applied fields (magnetic and electric), deflection, light, temperature change, acidity change, and molecular interaction detection. Reversible colours may be produced by altering the spacing between the particles, the filler materials, or the structural elements of the system’s refractive indices. This article briefly discusses the inner workings of CNCs, potential barriers to developing photonic structures, and several techniques and processes for achieving changeable colours.
]]>Applied Biosciences doi: 10.3390/applbiosci1030015
Authors: Pia S. Menezes Yakun Yan Yunjia Yang Neena Mitter Timothy J. Mahony Karishma T. Mody
Insects and ectoparasites are causes for major concern throughout the world due to their economic and welfare impacts on livestock agriculture. Current control measures involve chemicals such as acaricides which pose challenges like chemical resistance and longer withholding periods. To enable more sustainable agriculture practices, it is important to develop technologies that combine targeted effectiveness with minimal environmental footprint. RNA interference (RNAi) is a eukaryotic process in which transcript expression is reduced in a sequence-specific manner. This makes it a perfect tool for developing efficient and effective biological control against pests and pathogens. Double-stranded RNA (dsRNA) is the key trigger molecule for inducing RNAi; this concept is widely studied for development of RNA-based biopesticides as an alternative to chemical controls in crop protection for targeting pests and pathogens with accuracy and specificity. In this review, we discuss key advances made using RNAi technology and how they can be applied to improve health in livestock industries. This includes research focused on different delivery mechanisms of dsRNA, important developments in regulatory frameworks, and risk identification, that will enable the future adoption of RNAi technologies to improve animal health.
]]>Applied Biosciences doi: 10.3390/applbiosci1020014
Authors: Hironaga Akita Yoshiki Shinto Zen-ichiro Kimura
Microbiologically influenced corrosion (MIC) is caused by biofilms formed on metal surfaces, and MIC of metal alloys on marine infrastructure leads to severe accidents and great economic losses. Although bacterial community analyses of the biofilms collected from corroded metal have been studied, the analyses of biofilms collected from uncorroded metal are rarely reported. In this study, a biofilm formed on an uncorroded metal joint attached to a metal dock mooring at Akitsu Port was used as a model for bacterial community analysis. The bacterial community was analyzed by high-throughput sequencing of the V3–V4 variable regions of the 16S rRNA gene. Bacterial species contained in the biofilms were identified at the genus level, and Alkanindiges bacteria were the dominant species, which have been not reported as the dominant species in previous research on MIC. The genome sequences of known Alkanindiges bacteria do not have conserved gene clusters required to cause metal corrosion, which suggests that Alkanindiges bacteria do not corrode metals but act on the formation of biofilms. Those findings indicated that the bacterial community may change significantly during the process from biofilm formation to the occurrence of metal corrosion.
]]>Applied Biosciences doi: 10.3390/applbiosci1020013
Authors: Blanca Rojas-Sánchez Paulina Guzmán-Guzmán Luzmaria R. Morales-Cedeño Ma. del Carmen Orozco-Mosqueda Blanca C. Saucedo-Martínez Juan M. Sánchez-Yáñez Ayomide Emmanuel Fadiji Olubukola Oluranti Babalola Bernard R. Glick Gustavo Santoyo
The excessive use of agrochemicals in the field to increase production and counteract the negative effects caused by biotic and abiotic factors has led to a deterioration in soil fertility, plus an increment in negative impacts on the environment and human health. Therefore, the application of beneficial microorganisms as bioinoculants is an eco-friendly alternative to agrochemicals. Plant growth-promoting bacteria and fungi have been effective in promoting plant growth and production, as well as reducing the action of pathogens in multiple crops. However, successful application of such beneficial microorganisms in the agricultural field has faced several difficulties, such as survival, colonization efficiency and short periods of shelf storage. Therefore, it is essential to explore novel ways to encapsulate, formulate and apply bioinoculants. To obtain the expected quality in bioencapsulated products, it is essential to determine the type of polymer, capsule size, encapsulation technique and use the correct chemical and physical cofactors involved in the production process. Thus, this review highlights the various formulation types and application techniques, as well as discussing the multiple advantages of using microbial encapsulates to have better results in agricultural production.
]]>Applied Biosciences doi: 10.3390/applbiosci1020012
Authors: Marwa Amri Dina Mateus Marwa Gatrouni Mohamed Ridha Rjeibi Nedra Asses Chaabane Abbes
In the previous half-century, natural rock phosphates (PN) have been a valuable alternative for phosphorus (P) fertilizer for sustainable agriculture; furthermore, phosphogypsum (PG) has been widely used as a soil amendment fertilizer since it improves some soil properties, increases crop yields, and represents an environmental concern that can make a good economic profit; this research aimed to study the effects of microbial consortia of phosphate-solubilizing microorganisms (PSM) on the solubilization of PN and PG in the soil, and their effects on promoting plant growth and nutrient assimilation using ryegrass as a plant model. Local supply of PG with Pseudomonas fluorescens (MW165744) significantly increases root proliferation and plant biomass dry weight compared to other isolates, as well as improves total P uptake, with a maximum value of 62.31 mg/pot. The opposite occurred in mixing inoculation with Pseudomonas fluorescens, Pantoea agglomerans (MW165752) and Stenotrophomonas maltophilia (MW221274), with a negligible total P assimilation of 5.39 mg/pot. Whereas the addition of Pseudomonas agglomerans with PG gave outstanding total P absorption of 57.05 mg/pot when compared with PN input of 38.06 mg/pot. Finally, the results prove that the co-inoculation of Pseudomonas fluorescens with PG could be a promising and alternative option to use it as a source of P fertilizer for plants and to maintain a high level of nutrients in the soil.
]]>Applied Biosciences doi: 10.3390/applbiosci1020011
Authors: You Lv Shan Zheng Adi Goldenzweig Fengjiang Liu Yan Gao Xiuna Yang Ajit Kandale Ross P. McGeary Simon Williams Bostjan Kobe Mark A. Schembri Michael J. Landsberg Bin Wu Thomas B. Brück Volker Sieber Mikael Boden Zihe Rao Sarel J. Fleishman Gerhard Schenk Luke W. Guddat
The branched-chain amino acids (BCAAs) leucine, isoleucine and valine are synthesized via a common biosynthetic pathway. Ketol-acid reductoisomerase (KARI) is the second enzyme in this pathway. In addition to its role in BCAA biosynthesis, KARI catalyzes two rate-limiting steps that are key components of a cell-free biofuel biosynthesis route. For industrial applications, reaction temperature and enzyme stability are key factors that affect process robustness and product yield. Here, we have solved the cryo-EM structure (2.94 Å resolution) of a homododecameric Class I KARI (from Campylobacter jejuni) and demonstrated how a triad of amino acid side chains plays a crucial role in promoting the oligomerization of this enzyme. Importantly, both its thermal and solvent stability are greatly enhanced in the dodecameric state when compared to its dimeric counterpart (apparent melting temperatures (Tm) of 83.1 °C and 51.5 °C, respectively). We also employed protein design (PROSS) for a tetrameric Class II KARI (from Escherichia coli) to generate a variant with improved thermal and solvent stabilities. In total, 34 mutations were introduced, which did not affect the oligomeric state of this enzyme but resulted in a fully functional catalyst with a significantly elevated Tm (58.5 °C vs. 47.9 °C for the native version).
]]>Applied Biosciences doi: 10.3390/applbiosci1020010
Authors: Chiemela S. Odoemelam Elena Hunter John Simms Zeeshan Ahmad Ming-Wei Chang Benita Percival Ian H. Williams Marco Molinari Shina Caroline Lynn Kamerlin Philippe B. Wilson
The glucagon-like peptide 1 receptor (GLP-1R) is a member of the family (or class) B G-protein-coupled receptor (GPCR). The receptor is a regulator of insulin and a key target in treating Type 2 diabetes mellitus. In this investigation, computational chemistry techniques such as molecular docking were combined with in silico ADME/Tox predictions to determine the position and structure of the allosteric binding site, as well as to examine how the allosteric modulators bind to the binding site. In silico evaluation was used to evaluate the ADME/Tox properties of the allosteric modulators. The findings of the ligand docking studies suggest that the allosteric binding site is situated around the transmembrane (TM) domain TM 6 of the receptor in the active state. ADME/Tox characterisation of the allosteric modulators demonstrate that compounds 1–3 (2,6,7-trichloro-3-(trifluoromethyl)quinoxaline, 1-(5-(4-(tert-butyl)phenyl)-1,3,4-oxadiazol-2-yl)-6,6-dimethyl-3-(methylsulfonyl)-6,7-dihydrobenzo[c]thiophen-4(5H)-one, 2-((4-chlorophenyl)thio)-3-(trifluoromethyl)quinoxaline, respectively) complied with the traditional method of evaluating drug-likeness; Lipinski’s rule of 5. The allosteric modulator compound 4 (3-(8-chloro-6-(trifluoromethyl)imidazo[1,2-a]pyridin-2-yl)phenyl cyclohexanecarboxylate) failed to comply with Lipinski’s rule of five as a result of having a logP value of over 5.6. Moreover, molecular docking studies provide insights into potential allosteric binding sites and possible interactions. Finally, the in silico ADME/Tox study results are described as relevant to developing a viable drug candidate.
]]>Applied Biosciences doi: 10.3390/applbiosci1020009
Authors: Susana Santos Braga
This review addresses the search for activity enhancement of leishmanicidal organic compounds through their coordination chemistry with ruthenium. In an introduction to leishmaniasis, its clinical manifestations, geographical distribution, available forms of treatment, and challenges to disease management are presented. Ruthenium complexes, owing to their physico-chemical and biological properties, are introduced as a suitable molecular library from which to find alternatives to current medicines. The main sections of the review describe complexes reported in the literature, organised into two main groups: organometallics and inorganic complexes. The activity of the ruthenium complexes is presented compared with that of the ligands for a critical assessment of their utility in future clinical application.
]]>Applied Biosciences doi: 10.3390/applbiosci1020008
Authors: Robert J. Henry
The genome sequence of any organism is key to understanding the biology and utility of that organism. Plants have diverse, complex and sometimes very large nuclear genomes, mitochondrial genomes and much smaller and more highly conserved chloroplast genomes. Plant genome sequences underpin our understanding of plant biology and serve as a key platform for the genetic selection and improvement of crop plants to achieve food security. The development of technology that can capture large volumes of sequence data at low costs and with high accuracy has driven the acceleration of plant genome sequencing advancements. More recently, the development of long read sequencing technology has been a key advance for supporting the accurate sequencing and assembly of chromosome-level plant genomes. This review explored the progress in the sequencing and assembly of plant genomes and the outcomes of plant genome sequencing to date. The outcomes support the conservation of biodiversity, adaptations to climate change and improvements in the sustainability of agriculture, which support food and nutritional security.
]]>Applied Biosciences doi: 10.3390/applbiosci1020007
Authors: Timothy A. G. Langrish
This review highlights the involvement of mass transfer in animal food-digestion processes. There may be several mass-transfer steps during the dissolution of food components, starting from the food itself, moving into the digestive juices, then moving through the walls of the gastrointestinal tract. These steps create a sequence of film resistances to mass transfer, where one film resistance often limits the overall mass-transfer process. Mass-transfer rates, mass-transfer coefficients, and the time scales and time constants for different parts of the food-digestion process are all interlinked, and the connections have been explained. In some parts of the food-digestion process, the time constants for the mass-transfer process are similar to the residence times for food digestion, emphasising the importance of mass transfer in these parts of food digestion, such as the duodenum. The mass-transfer and transport behaviour for in vivo human digestive systems and in vitro guts-on-a-chip may be very similar, suggesting that cells on the intestine walls, whether in vitro (guts-on-a-chip) or in vivo, may see similar transport behaviour for both nutrients towards the cells, and waste products away from them.
]]>Applied Biosciences doi: 10.3390/applbiosci1010006
Authors: Francesco Cappello Dario Saguto Stefano Burgio Letizia Paladino Fabio Bucchieri
In this brief Opinion paper, the term “muco-microbiotic layer” is introduced to describe the innermost layer of the intestinal wall. This layer may contribute not only to the overall health of the bowel, but also to that of extraintestinal organs. Its constituents, in terms of soluble molecules and nanovesicles, need to be studied further. Moreover, one can hypothesize the existence of an analogous layer in other organs, such as the airways or some parts of the genital tracts. Further studies on it are needed.
]]>Applied Biosciences doi: 10.3390/applbiosci1010005
Authors: Piergiorgio Cianciullo Francesca Cimmino Viviana Maresca Sergio Sorbo Paola Bontempo Adriana Basile
Bryophytes are a poorly studied group of land plants that have been used in traditional medicine as a multipurpose remedy for centuries. Due to their peculiar morphology and physiology, bryophytes synthesise a multitude of secondary metabolites with a wide range of nutraceutical and pharmaceutical activities. Research has highlighted that secondary metabolites in bryophytes can also act as antitumour agents. Several studies have shown that bryophyte extracts and pure metabolites are cytotoxic against many cancer cell lines. Interestingly, some of these molecules and their derivatives are capable of acting on a specific target in cancer cells. Some macrocyclic(bis)bibenzyls from bryophytes can inhibit P-glycoprotein, reverting multidrug resistant cancer cell phenotypes, induce depolymerization of tubulin, stimulate apoptotic pathways, and inhibit angiogenesis. This brief review aims to collect recent knowledge on secondary metabolites of bryophytes and their derivatives, which have demonstrated an interaction with different molecular processes in cancer cells.
]]>Applied Biosciences doi: 10.3390/applbiosci1010004
Authors: Lorenza Destro Ross Van Melsen Alex Gobbi Andrea Terzi Matteo Genitoni Alfonso Zambon
Functionalized pyrazole-urea scaffolds are a common type II chemotype for the inhibition of protein kinases (PKs), binding simultaneously into the ATP-binding pocket with an ATP bioisostere and into a vicinal allosteric pocket with a pyrazole group. Standard approaches to the scaffold require multi-step synthesis of the ATP bioisostere followed by phosgene or triphosgene-mediated coupling with the substituted pyrazole group. Here we report an expedient approach to the chemotype, characterized by an optimized MW-assisted Suzuki coupling on easily accessed bromo-phenyl pyrazole ureas. The new protocol allowed quick access a large library of target analogues covering a broad chemical space of putative protein kinases inhibitors (PKIs).
]]>Applied Biosciences doi: 10.3390/applbiosci1010003
Authors: Valme Jurado Jose Luis Gonzalez-Pimentel Angel Fernandez-Cortes Tamara Martin-Pozas Roberto Ontañon Eduardo Palacio Bernardo Hermosin Sergio Sanchez-Moral Cesareo Saiz-Jimenez
European caves contain some of the world’s greatest Paleolithic paintings, and their conservation is at risk due to the use of artificial lighting. Both lighting and high CO2 promotes the growth of phototrophic organisms on walls, speleothems and ground sediments. In addition, the combined effect of increases in CO2, vapor concentration and temperature variations induced by visitors can directly affect the development of corrosion processes on the cave rock surfaces. An early detection of the occurrence of phototrophic biofilms on Paleolithic paintings is of the utmost importance, as well as knowing the microorganisms involved in the colonization of rocks and walls. Knowledge of the colonizing species and their ecology will allow the adoption of control measures. However, this is not always possible due to the limited amount of biomass available for molecular analyses. Here, we present an alternative approach to study faint green biofilms of Chlorophyta in the initial stage of colonization on the Polychrome Panel in El Castillo Cave, Cantabria, Spain. The study of the biofilms collected on the rock art panel and in the ground sediments revealed that the lighting of the cave promoted the development of the green algae Jenufa and Coccomyxa, as well as of complex prokaryotic and eukaryotic communities, including amoebae, their endoparasites and associated bacteria and fungi. The enrichment method used is proposed as a tool to overcome technical constraints in characterizing biofilms in the early stages, allowing a preliminary characterization before deciding for direct or indirect interventions in the cave.
]]>Applied Biosciences doi: 10.3390/applbiosci1010002
Authors: Robert J. Henry
The 21st century has been defined as the age of biology [...]
]]>Applied Biosciences doi: 10.3390/applbiosci1010001
Authors: Aref Abbasi Moud
Cellulose, a linear polysaccharide, is the most common and renewable biopolymer in nature. Because this natural polymer cannot be melted (heated) or dissolved (in typical organic solvents), making complicated structures from it necessitates specialized material processing design. In this review, we looked at the literature to see how cellulose in various shapes and forms has been utilized in conjunction with microfluidic chips, whether as a component of the chips, being processed by a chip, or providing characterization via chips. We utilized more than approximately 250 sources to compile this publication, and we sought to portray cellulose manufacturing utilizing a microfluidic system. The findings reveal that a variety of products, including elongated fibres, microcapsules, core–shell structures and particles, and 3D or 2D structured microfluidics-based devices, may be easily built utilizing the coupled topics of microfluidics and cellulose. This review is intended to provide a concise, visual, yet comprehensive depiction of current research on the topic of cellulose product design and understanding using microfluidics, including, but not limited to, paper-based microfluidics design and implications, and the emulsification/shape formation of cellulose inside the chips.
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