Appl. Biosci., Volume 1, Issue 2 (September 2022) – 8 articles

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. Full article

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. Full article

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. Full article

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). Full article

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. Full article

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. Full article

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. Full article

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. Full article