BioTech, Volume 11, Issue 4 (December 2022) – 13 articles

Fourier Transform InfraRed spectroscopy of serum and plasma has been highly explored for medical diagnosis, due to its general simplicity, and high sensitivity and specificity. To evaluate the plasma and serum molecular fingerprint, as obtained by FTIR spectroscopy, to acquire the system metabolic state, serum and plasma spectra were compared to characterize the metabolic state of 30 human volunteers, between 90 days consumption of green tea extract rich in Epigallocatechin-3-gallate (EGCG). Both plasma and serum spectra enabled the high impact of EGCG consumption on the biofluid spectra to be observed, as analyzed by the spectra principal component analysis, hierarchical-cluster analysis, and univariate data analysis. Plasma spectra resulted in the prediction of EGCG consumption with a slightly higher specificity, accuracy, and precision, also pointing to a higher number of significant spectral bands that were different between the 90 days period. Despite this, the lipid regions of the serum spectra were more affected by EGCG consumption than the corresponding plasma spectra. Therefore, in general, if no specific compound analysis is highlighted, plasma is in general the advised biofluid to capture by FTIR spectroscopy the general metabolic state. If the lipid content of the biofluid is relevant, serum spectra could present some advantages over plasma spectra. Full article

The ferulic acid (FA)-oxidation by Myceliophthora thermophila laccase was performed in phosphate buffer at 30 °C and pH 7.5 as an eco-friendly procedure. LC-MS analysis showed that oxidation products were four dehydrodimers (P1, P2, P3, P5) at MM = 386 g/mol, two dehydrotetramers (P6, P7) at MM = 770 g/mol and one decarboxylated dehydrodimer (P4) at MM = 340 g/mol. Structural characterization showed that FA-dehydrodimers were symmetric for P1 and P5 while asymmetric for P2, P3 and P4. Physicochemical characterization showed that oxidation products presented a higher lipophilicity than that of FA. Moreover, symmetric dimers and tetra dimers had a higher melting point compared to FA and its asymmetric dimers. Antioxidant and anti-proliferative assessments indicated that enzymatic oligomerization increased antioxidant and anti-proliferative properties of oxidation products for P2, P3 and P6 compared to FA. Finally, this enzymatic process in water could produce new molecules, having good antiradical and anti-proliferative activities. Full article

Falcipain-2 (FP-2) is one of the main haemoglobinase of P. falciparum which is an important molecular target for the treatment of malaria. In this study, we have screened alkaloids to identify potential inhibitors against FP-2 since alkaloids possess great potential as anti-malarial agents. A total of 340 alkaloids were considered for the study using a series of computational pipelines. Initially, pharmacokinetics and toxicity risk assessment parameters were applied to screen compounds. Subsequently, molecular docking algorithms were utilised to understand the binding efficiency of alkaloids against FP-2. Further, oral toxicity prediction was done using the pkCSM tool, and 3D pharmacophore features were analysed using the PharmaGist server. Finally, MD simulation was performed for Artemisinin and the top 3 drug candidates (Noscapine, Reticuline, Aclidinium) based on docking scores to understand the functional impact of the complexes, followed by a binding site interaction residues study. Overall analysis suggests that Noscapine conceded good pharmacokinetics and oral bioavailability properties. Also, it showed better binding efficiency with FP-2 when compared to Artemisinin. Interestingly, structure alignment analysis with artemisinin revealed that Noscapine, Reticuline, and Aclidinium might possess similar biological action. Molecular dynamics and free energy calculations revealed that Noscapine could be a potent antimalarial agent targeting FP-2 that can be used for the treatment of malaria and need to be studied experimentally in the future. Full article

Members of the phylum Actinomycetota (formerly Actinobacteria) have historically been the most prolific providers of small bioactive molecules. Although the genus Streptomyces is the best-known member for this issue, other genera, such as Gordonia, have shown interesting potential in their specialized metabolism. Thus, we combined herein the result of a comprehensive literature survey on metabolites derived from Gordonia strains with a comparative genomic analysis to examine the potential of the specialized metabolism of the genus Gordonia. Thirty Gordonia-derived compounds of different classes were gathered (i.e., alkaloids, amides, phenylpropanoids, and terpenoids), exhibiting antimicrobial and cytotoxic activities, and several were also isolated from Streptomyces (e.g., actinomycin, nocardamin, diolmycin A1). With the genome data, we estimated an open pan-genome of 57,901 genes, most of them being part of the cloud genome. Regarding the BGCs content, 531 clusters were found, including Terpenes, RiPP-like, and NRPS clusters as the most frequent clusters. Our findings demonstrated that Gordonia is a poorly studied genus in terms of its specialized metabolism production and potential applications. Nevertheless, given their BGCs content, Gordonia spp. are a valuable biological resource that could expand the chemical spectrum of the phylum Actinomycetota, involving novel BGCs for inspiring innovative outlines for synthetic biology and further use in biotechnological initiatives. Therefore, further studies and more efforts should be made to explore different environments and evaluate other bioactivities. Full article

Beet yellows virus, which belongs to the genus Closterovirus, family Closteroviridae and has a significant negative economic impact, has proven to be challenging to detect and diagnose. To obtain antibodies against BYV, we propose an easier bioinformatics approach than the isolation and purification of the wild virus as an antigen. We used the SWISS-MODEL Workspace (Biozentrum Basel) protein 3D prediction program to discover epitopes of major coat protein p22 lying on the surface of the BYV capsid. Sequences coding these epitopes were cloned into plasmid pQE-40 (Qiagen) in frame with mouse dihydrofolate reductase gene. Fused epitopes were expressed in Escherichia coli and isolated by the Ni-NTA affinity chromatography. Murine antibodies were raised against each epitope and in a combination of both and characterized by dot-ELISA and indirect ELISA. We successively used these antibodies for diagnosis of virus disease in systemically infected Tetragonia tetragonioides. We believe the approach described above can be used for diagnostics of difficult-to-obtain and hazardous-to-health viral infections. Full article

Biofilters are biological air-phase packed-bed reactors used for the removal of industrial air pollutants such as volatile organic compounds (VOCs) and odors. Because of the economic and environmental benefits, biofilter technology is preferred in applications such as wastewater treatment plants, waste recycling facilities, and several chemical industries over conventional treatment methods such as adsorption, absorption, and thermal oxidation processes. In order to predict the performance of biofilters, mathematical models under steady-state and transient conditions are needed. The transient biofilter models for gas-phase bioreactors are highly complex, as they involve several parameters that are not easily determined for industrial applications. In this work, a practical transient biofilter model is developed and an analytical solution for the transient model is obtained. When this model is compared with the published but more complex model, this new transient model produces almost the same level of prediction with equal comparisons of experimental data for VOCs, benzene, and toluene. This simple model has fewer parameters and will be very useful and practical for industrial applications for the analysis of transient biofilter performance. Full article

Background: Functional Abdominal Pain disorders (FAPDs) are a group of heterogeneous gastrointestinal disorders with unclear pathophysiology. In children, FAPDs are more common in the winter months than summer months. The possible influence of school stressors has been proposed. Previously, our group showed differences in bacterial relative abundances and alpha diversity in the gut microbiome and its relationship with stressors in a cross-sectional evaluation of children suffering from FAPDs compared to a healthy control group. We present longitudinal data to assess whether the gut microbiome changes over school terms in the control and FAPDs groups. Methods: The longitudinal study included children with FAPDs (n = 28) and healthy controls (n = 54). Gastrointestinal symptoms, as well as stool microbiome, were assessed in both groups. Stool samples were serially collected from all participants during both the school term and summer vacation. The stool samples were subjected to total genomic extraction, 16S rRNA amplicon sequencing, and bioinformatics analysis. The gut microbiome was compared at school and during vacation. Other metrics, alpha diversity, and beta diversity, were also compared between the two school terms in every group. Results: In the healthy group, there were differences in microbiome composition between school terms and summer vacation. Conversely, we found no differences in the FAPDs group between the two terms. The healthy control group revealed differences (p-value < 0.05) in 55 bacterial species between the school term and vacation. Several of the differentially abundant identified bacteria were involved in short-chain fatty acids production (SCFAs), inflammation reduction, and gut homeostasis. Alpha diversity metrics, such as the Shannon index, were different in the control group and remained unchanged in the FAPDs group. Conclusion: Although preliminary, our findings suggest that the gut microbiome is static in FAPDs. This compares with a more dynamic healthy gut microbiome. Further studies are warranted to corroborate this and understand the interplay between stress, symptoms, and a less diverse and static microbiome. Future studies will also account for different variables such as diet and other patient demographic criteria that were missing in the current study. Full article

Light can be used to regulate protein interactions with a high degree of spatial and temporal precision. Photo-switchable systems therefore allow the development of controllable protein complexes that can influence various cellular and molecular processes. Here, we describe a plant virus-based nanoparticle shuttle for the distribution of proteins that can be released when exposed to light. Potato virus X (PVX) is often used as a presentation system for heterologous proteins and epitopes, and has ideal properties for biomedical applications such as good tissue penetration and the ability to form hydrogels that present signaling molecules and promote cell adhesion. In this study, we describe three different systems attached to the surface of PVX particles: LOVTRAP, BphP1/QPAS1 and Dronpa145N. We demonstrated the functionality of all three photo-switchable protein complexes in vitro and the successful loading and unloading of PVX particles. The new systems provide the basis for promising applications in the biomedical and biomaterial sciences. Full article

Tomato production is severely affected by abiotic stresses (drought, flood, heat, and salt) and causes approximately 70% loss in yield depending on severity and duration of the stress. Drought is the most destructive abiotic stress and tomato is very sensitive to the drought stress, as cultivated tomato lack novel gene(s) for drought stress tolerance. Only 20% of agricultural land worldwide is irrigated, and only 14.51% of that is well-irrigated, while the rest is rain fed. This scenario makes drought very frequent, which restricts the genetically predetermined yield. Primarily, drought disturbs tomato plant physiology by altering plant–water relation and reactive oxygen species (ROS) generation. Many wild tomato species have drought tolerance gene(s); however, their exploitation is very difficult because of high genetic distance and pre- and post-transcriptional barriers for embryo development. To overcome these issues, biotechnological methods, including transgenic technology and CRISPR-Cas, are used to enhance drought tolerance in tomato. Transgenic technology permitted the exploitation of non-host gene/s. On the other hand, CRISPR-Cas9 technology facilitated the editing of host tomato gene(s) for drought stress tolerance. The present review provides updated information on biotechnological intervention in tomato for drought stress management and sustainable agriculture. Full article

Microflora is actively used to produce value-added materials in industry, and each cell density should be controlled for stable microflora use. In this study, a simple system evaluating the cell density was constructed with artificial intelligence (AI) using the absorbance spectra data of microflora. To set up the system, the prediction system for cell density based on machine learning was constructed using the spectra data as the feature from the mixture of Saccharomyces cerevisiae and Chlamydomonas reinhardtii. As the results of predicting cell density by extremely randomized trees, when the cell densities of S. cerevisiae and C. reinhardtii were shifted and fixed, the coefficient of determination (R²) was 0.8495; on the other hand, when the cell densities of S. cerevisiae and C. reinhardtii were fixed and shifted, the R² was 0.9232. To explain the prediction system, the randomized trees regressor of the decision tree-based ensemble learning method as the machine learning algorithm and Shapley additive explanations (SHAPs) as the explainable AI (XAI) to interpret the features contributing to the prediction results were used. As a result of the SHAP analyses, not only the optical density, but also the absorbance of the Soret and Q bands derived from the chloroplasts of C. reinhardtii could contribute to the prediction as the features. The simple cell density evaluating system could have an industrial impact. Full article

Omicron BA.2.75 may become the next globally dominant strain of COVID-19 in 2022. The BA.2.75 sub-variant has acquired more mutations (9) in spike protein and other genes of SARS-CoV-2 than any other variant. Thus, its chemical composition and thermodynamic properties have changed compared with earlier variants. In this paper, the Gibbs energy of the binding and antigen-receptor binding rate was reported for the BA.2.75 variant. Gibbs energy of the binding of the Omicron BA.2.75 variant is more negative than that of the competing variants BA.2 and BA.5. Full article

The microbial fuel cell has been considered a promising alternative to traditional fossil energy. It has great potential in energy production, waste management, and biomass valorization. However, it has several technical issues, such as low power generation efficiency and operational stability. These issues limit the scale-up and commercialization of MFC systems. This review presents the latest progress in microbial community selection and genetic engineering techniques for enhancing microbial electricity production. The summary of substrate selection covers defined substrates and some inexpensive complex substrates, such as wastewater and lignocellulosic biomass materials. In addition, it also includes electrode modification, electron transfer mediator selection, and optimization of operating conditions. The applications of MFC systems introduced in this review involve wastewater treatment, production of value-added products, and biosensors. This review focuses on the crucial process of microbial fuel cells from preparation to application and provides an outlook for their future development. Full article