Appl. Biosci., Volume 3, Issue 4 (December 2024) – 10 articles

This article describes the basics of chemical thermodynamics and its application to the study of plant biomass and its main components, cellulose, hemicelluloses, lignin, etc. The energy potential of various biomass types, as well as biomass-based solid, liquid, and gaseous biofuels, is determined. A method of additive contributions of combustion enthalpies of main components is proposed to calculate the combustion enthalpy of biomass samples. It is also established that the potential of thermal energy of the initial biomass is higher than the energy potential of secondary biofuels released from this biomass. The thermodynamic functions of plant biopolymers are calculated. Moreover, the thermodynamic stability of various crystalline allomorphs of cellulose and amorphous cellulose is studied. The melting enthalpies of crystallites with different types of crystalline structures are estimated. A thermochemical method for determining the degree of crystallinity of cellulose is proposed. The most important biomass components are cellulose and other polysaccharides. The thermodynamics of the enzymatic hydrolysis of polysaccharides and their conversion into glucose are described. In addition, the thermodynamic analysis of the conversion process of glucose into bioethanol is performed. Considerable attention is also paid to the thermochemistry of cellulose alkalization, etherification, and esterification. Full article

Cultivated yam (Dioscorea rotundata) is a staple tuber crop in West Africa which is mainly vegetatively propagated. Although the majority of yam cultivars flower, the control of their sexual reproduction remains largely unknown despite its importance for plant-breeding programs. While described as a dioecious species, yam has several monoecious (mix) cultivars that are often subject to spontaneous sex changes. This study aims to evaluate the impact of phytohormones on sex expression and flower development in cultivated yams D. rotundata. Exogenous applications of 1 mM 6-benzylaminopurine (BAP) and 1 mM methyl jasmonate (MeJa) were performed on seedlings of female (Gnidou, Anago), male (Flou) and mix (Katala and Laboko) cultivars. The mix cultivars produced monoecious, male and female plants while the female and male cultivars had rather stable sex. Our results showed that MeJa exhibited a significant masculinising effect in mix cultivars and induced inflorescence and flower malformations in female cultivars (56% in Gnidou and 37% in Anago). Most malformations were inflorescence branching and sterile flowers (non-differentiated ovary) with extra cycles of sepals. Moreover, MeJa reduced flowering time in the cultivars of all sexes and increased the number of inflorescences per plant as well as the number of flowers per plant. Our results showed that BAP reduced the flowering time, synchronized flowering in female plants and increased the number of inflorescences per plant in monoecious plants. However, our results did not allow for strong conclusions regarding the effect of BAP on sex expression due to the high proportion of female flowering in both the control and BAP-sprayed plants. Nevertheless, we did not observe any masculinising effect for BAP. Further research that would highlight hormone and homeotic gene interactions in flowering could be of key interest in understanding the hormonal control of sex in cultivated yams D. rotundata. Full article

Microplastics (MPs), defined as plastic particles of less than 5 mm, pose a significant global environmental threat, particularly in aquatic ecosystems, due to their persistence and potential harmful effects on wildlife and human health. They can absorb persistent organic pollutants (POPs), like polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs), raising concerns about their impact on biota. To elucidate this impact, the present study employed attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) to analyse the characteristics of MPs sourced from commercial cosmetics. We investigated the toxicity of MPs on Caenorhabditis elegans and two entomopathogenic nematode species, Steinernema feltiae (the enviroCORE strain SB12(1)) and Steinernema carpocapsae (a commercial strain from e-NEMA) in laboratory bioassays. Nematodes were exposed to various concentrations of MPs and other pollutants, including atrazine, 1,3-dichloropropene, naphthalene, and fluorene, in controlled settings over 72 to 96 h. Additionally, high-throughput 18S rDNA sequencing was used to analyse nematode biodiversity in sediments from the River Barrow (RB) in SE Ireland. Our findings revealed that MPs increased nematode mortality and adversely affected community structure, as indicated by nematode maturity and sigma maturity indices, suggesting a potential disruption of the ecological balance in river sediments. This highlighted the ecological risks posed by MP pollution and emphasised the urgent need for further research into the health of benthic ecosystems in Ireland, particularly in relation to how MPs may influence nematode community dynamics and biodiversity. Full article

Rivers are crucial hydrological cycle components, supporting ecosystems and human activities. Managing and protecting river water quality is essential. Diatoms, microscopic algae, are widespread and sensitive to changes in water quality, making them effective bioindicators. This study focused on the Kuils River in the Western Cape, South Africa, where diatom sampling was conducted at four sites. Their communities are affected by different physicochemical parameters, such as changes in pH, salinisation, eutrophication, and organic enrichment. A total of 98 diatom species were identified. The Omnidia software was used to calculate the Generic Diatom Index, Specific Pollution Index, and Trophic Diatom Index. Historical physicochemical data such as pH, chemical oxygen demand, and phosphorus were obtained from the Department of Water and Sanitation between 2019 and 2021 and were used to provide a reference for comparing diatoms. The results showed clear signs of pollution, as shifts in diatom species composition were observed. Pollution-tolerant species such as the Nitzschia palea (Kützing) W Smith 1856, Navicula viridula (Kützing) Ehrenberg 1838, Eunotia bilunaris (Ehrenberg) Schaarschmidt 1880, and Ulnaria ulna (Nitzsch) Compère 2001 dominated, while less pollution-tolerant species like Gomphonema parvulum f.saprophilum Lange-Bertalot and E. Reichardt 1993 and Stephanocylus meneghinianus (Kutzing) Kulikovskiy, Genkal, and Kociolek 2022 were less abundant. Both diatom indices and physicochemical data indicated poor water quality in the Kuils River. The study concludes that diatoms are a valuable tool for biomonitoring river water quality and recommends their use alongside traditional physicochemical methods for future assessments of river systems. Full article

Distraction osteogenesis (DO) is a process which uses the bone’s natural healing tendencies to repair and lengthen pathologic, missing, or malformed bone. The mechanism of DO mimics the pathway that the body uses in any other fracture repair however the location of the fracture is carefully controlled by a surgical osteotomy. Postoperatively, the bone is allowed to begin its natural healing process, with the lengthener applying constant tension and thus re-initiating the process of healing along the length of the distraction gap. Current clinical indications for DO include limb length discrepancy, congenital bone length deformity, large bone defects, and extremity reconstruction due to hypoplasia or limb salvage procedures. The risks of DO include soft tissue complications, relapse or improper correction, cost or resource-related challenges, and psychosocial stigmas surrounding long treatment durations and the necessity of wearing the distraction lengthening hardware. Future directions for DO include supplements to the bone regeneration process (such as growth factors and/or mechanical stimulation) or improvements to the distractor device itself (changes in material and/or the structure of the device itself). This review aims to offer a comprehensive summary of the indications, underlying biological mechanisms, and practical considerations when implementing the use of distraction osteogenesis in clinical practice. Full article

Integrated crop and livestock systems (ICLSs) have been considered an important management-based decision to improve soil health by carbon sequestration. A two-year study (2019–2021) at CPBES in Newton, MS, was conducted to evaluate the effect of an ICLS on soil microbial diversity in the southeastern region of the USA, representing agroclimatic conditions that are warm and humid. Amplicons targeting bacterial 16S rRNA genes and fungal ITS2 regions were sequenced. Taxonomic assignment and characterization of microbial diversity were performed using QIIME2^®. Soil fungal diversity pattern showed significant difference (alpha diversity, p = 0.031 in 2020 and beta diversity, p = 0.037 in 2021). In contrast, no significant differences were observed in bacterial diversity. However, there were several beneficial bacterial phyla, such as Proteobacteria and Actinobacteria, and fungal phyla such as Ascomycota, which were dominant in both years and did not show significant differences due to cover crop treatments. Canonical Correspondence Analysis (CCA) and Mantel test showed significant influence on fungal diversity due to carbon (rm = 0.2581, p = 0.022), nitrogen (rm = 0.2921, p = 0.0165), and electrical conductivity (rm = 0.1836, p = 0.0583) in 2021, and on bacterial diversity due to EE-GRSP (rm = 0.22, p = 0.02) in 2020. However, the results showed that there were no significant differences between the cover crop treatments that were consistent over a two-year study period. However, the mix of different cover crops such as oats (Avena sativa L.), crimson clover (Trifolium incarnatum L.), and tillage radish (Raphanus sativus L.) demonstrated higher positive correlation and lower negative correlation with different bacterial and fungal phyla. Long term study of ICLS is suggested to understand the shift in microbiome that would help in understanding the role of cover crops and grazing in improving crop production sustainably. Full article

This study explores the interaction between Vemurafenib (VEM), a potent BRAF inhibitor, and calf thymus DNA (ctDNA) using a comprehensive array of biophysical and computational techniques. The primary objective is to understand the potential off-target effects of VEM on DNA, given its established role in melanoma therapy targeting the BRAF V600E mutation. The investigation employed methods such as ultraviolet–visible absorption spectroscopy, steady-state fluorescence, circular dichroism, isothermal titration calorimetry, and advanced molecular dynamics simulations. The results indicate that VEM interacts with DNA primarily through a minor groove-binding mechanism, causing minimal structural disruption to the DNA double helix. Viscosity measurements and melting temperature analyses further confirmed this non-intercalative mode of binding. Calorimetry data revealed an exothermic, thermodynamically favorable interaction between VEM and ctDNA, driven by both enthalpic and entropic factors. Finally, computer simulations identified the most probable binding site and mode of VEM within the minor groove of the nucleic acid, providing a molecular basis for the experimental findings. Full article

Osteoarthritis is a joint disease that causes pain, stiffness, and reduced joint function because the protective cushioning inside the joints, called cartilage, gradually wears away. This condition is caused by various factors and complex processes in the joint’s environment, involving different types of cells producing factors that can either maintain the joint health or contribute to osteoarthritis. This study aimed to understand the factors influencing both healthy and diseased joints in DDD strategies for the in vitro preconditioning of MSCs. An electronic search in the PubMed, Scopus, and Web of Science databases was carried out using the terms (cartilage OR chondr*) AND (repair OR regeneration OR healing) AND (niche OR microenvironment)) AND (“growth factor” OR GF OR cytokine). Researchers used various methods, including macroscopic examinations, histology, immunohistochemistry, and microCT. Molecules associated with joint inflammation were identified, like macrophage markers, MMP-13, TNF, apoptotic markers, and interleukins. Chondrogenesis-related factors such as aggrecan GAG, collagen type II, and TGF beta family were also identified. This study suggests that balancing certain molecules and ensuring the survival of joint chondrocytes could be crucial in improving the condition of osteoarthritic joints, emphasizing the importance of chondrocyte survival and activity. Future preconditioning methods for MSC- and EV-based therapies can find suitable strategies in the described microenvironments to explore co-culture systems and soluble or extracellular matrix factors. Full article

Metallo-β-lactamases (MBLs) are members of the structurally conserved but functionally diverse MBL-fold superfamily of metallohydrolases. MBLs are a major concern for global health care as they efficiently inactivate β-lactam antibiotics, including the “last-resort” carbapenems, and no clinically suitable inhibitors are currently available. Increasingly, promiscuous β-lactamase activity is also observed in other members of the superfamily, including from viruses, which represents an underexplored reservoir for future pathways to antibiotic resistance. Here, two such MBL-fold enzymes from Bacillus phages, the cyclic mononucleotide-degrading proteins Apyc_Goe3 and Apyc_Grass, are shown to degrade β-lactam substrates efficiently in vitro. In particular, Apyc_Grass displays a distinct preference for carbapenem substrates with a catalytic efficiency that is within one order of magnitude of the clinically relevant MBL NDM-1. Mutagenesis experiments also demonstrate that the loss of a metal-bridging aspartate residue reduces nuclease activity up to 35-fold but improves carbapenemase activity. In addition, we hypothesise that the oligomeric state significantly influences β-lactamase activity by modifying access to the active site pocket. Together, these observations hint at a possible new avenue of resistance via the spread of phage-borne MBL-fold enzymes with β-lactamase activity. Full article

Papaya is a globally important crop, with production primarily based on hermaphrodite plants. Papaya has three sex types—male, female, and hermaphrodite—determined by flower morphology, but this is only distinguishable at the flowering stage. In this study, a recombinase polymerase amplification (RPA) assay was developed and optimized to identify the three sexes of papaya. Recombinant uvsX, uvsY, gp32, and Bsu DNA polymerase were used to study the effects of temperature, reaction time, and sensitivity conditions for RPA reaction efficiency. The optimal conditions were found to be 41 °C and a 30 min reaction time, allowing the detection of the target sex from specific DNA markers, even when using crude extract. This study shows that RPA could be used for sex determination in papaya, and the findings could contribute to developing a point-of-need strategy due to their sensitivity and specificity. Full article