Volume 22, Issue 3

The emergence of new variants of SARS-CoV-2, including Alpha, Beta, Gamma, Delta, Omicron variants, and XBB sub-variants, contributes to the number of coronavirus cases worldwide. SARS-CoV-2 is a positive RNA virus with a genome of 29.9 kb that encodes four structural proteins: spike glycoprotein (S), envelope glycoprotein (E), membrane glycoprotein (M), and nucleocapsid glycoprotein (N). These proteins are vital for viral activity, with the S protein facilitating attachment and membrane fusion through the receptor-binding domain (RBD) located in the S1 subunit. The RBD recognizes and binds to the human angiotensin-converting enzyme 2 (ACE-2) protein. An immunoinformatic-aided design of a peptide-based multiepitope vaccine candidate targeting the RBD glycoprotein is constructed from the SARS-CoV-2 sequence data base from various regions of Indonesia (Jakarta, West Java, and Bali). The results show that the RBD region of with accession ID EPI_ISL_15982641 from West Java had the highest antigenicity of 0.5904. This isolate is non-toxic and non-allergenic and shows a total of 18 LBL epitopes, 72 CTL epitopes, and 98 HTL epitopes. The epitope that has the best overall binding affinity was GCHNKCAY for MHC-I and GGCVFSYVGCHNKCAYWV for MHC-II which show a binding affinity of −13.6 and −15.5 (kcal/mol), respectively. Therefore, this study aims to design an epitope vaccine candidate based on samples from Indonesia that has good characteristics and may have the potential to stimulate an immune response against SARS-CoV-2.

This study investigates the gut microbiome and metabolome of asthma patients treated with inhaled corticosteroids (ICS), some of whom experience adverse side effects. We analyzed stool samples from 24 participants, divided into three cohorts: asthma patients with side effects, those without, and healthy controls. Using next-generation sequencing and LC-MS/MS metabolomics, we identified significant differences in bacterial species and metabolites. Multi-Omics Factor Analysis (MOFA) and Global Sensitivity Analysis-Partial Rank Correlation Coefficient (GSA-PRCC) provided insights into key contributors to side effects, such as tryptophan depletion and altered linolenate and glucose-1-phosphate levels. The study proposes dietary or probiotic interventions to mitigate side effects. Despite the limited sample size, these findings provide a basis for personalized asthma management approaches. Further studies are required to confirm initial fundings.

Lignin, the second most abundant plant biopolymer on Earth, is produced in large quantities as waste material by many industries. Researchers have studied bacterial metabolic networks as potential candidates for integrating lignin into a biotechnological value chain. The GEM used in this work for metabolic engineering is iNovo479, which simulates the metabolism of Novosphingobium aromaticivorans DSM12444. We have conducted a study on PDC production and found several intervention strategies to help achieve this goal. These strategies include more than just blocking the ligI gene, which has been a well-known approach. Although these new strategies resulted in a lower yield of PDC relative to biomass formed, they led to a higher cell yield than deleting the ligI gene. The research presented in this paper focuses on the production of high-value compounds from lignin. Previous studies have used mutated microorganisms to produce these bioproducts from large amounts of glucose. However, biosynthesis from lignin would improve productivity and make the fermentation process more cost-effective. Through gene knockouts, we have discovered ways to ensure a minimum production of bioproducts such as acetaldehyde, citrate, glutarate, glycerol, phenol, and propanoate when growing the N. aromaticivorans strain using lignin-derived compounds as unique substrates.

Appetite is an instinct that has been formed through evolution. Appetite promotes normal growth and development in humans. However, under conditions of food abundance, appetite can become excessive, posing significant health risks. In this study we have identified 80 human genes whose orthologs regulated food intake in model animal species. More than 80 % of these genes encode G-protein-coupled receptors and 29 % were found to be involved in developmental processes. Using phylostratigraphic age index (PAI), which specifies the evolutionary age of a gene, we found that this set of 80 genes contains an increased proportion of genes with the same phylostratigraphic age (PAI = 6, the stage of Vertebrata divergence) indicating the coordinated evolution of this group of genes. Using divergence index (DI), which indicates the type of selection to which the gene is subjected, we observed significant enrichment for genes with DI ≤ 0.25, i.e., those that are subject to strong stabilizing selection. The subgroup of genes having DI ≤ 0.25 included 45 genes and was enriched with genes that are associated with developmental processes. This finding supports the hypothesis that developmental disturbances generally impose strong constraints on viability due to purifying selection.