Comparative genomics of food-derived probiotic Lactiplantibacillus plantarum K25 reveals its hidden potential, compactness, and efficiency

This study aimed to investigate the intricate genetic makeup of the Lactiplantibacillus plantarum K25 strain by conducting a comprehensive analysis of comparative genomics. The results of our study demonstrate that the genome exhibits a high-level efficiency and compactness, comprising a total of 3,199 genes that encode proteins and a GC content of 43.38%. The present study elucidates the evolutionary lineage of Lactiplantibacillus plantarum strains through an analysis of the degree of gene order conservation and synteny across a range of strains, thereby underscoring their closely interrelated evolutionary trajectories. The identification of various genetic components in the K25 strain, such as bacteriocin gene clusters and prophage regions, highlights its potential utility in diverse domains, such as biotechnology and medicine. The distinctive genetic elements possess the potential to unveil innovative therapeutic and biotechnological remedies in future. This study provides a comprehensive analysis of the L. plantarum K25 strain, revealing its remarkable genomic potential and presenting novel prospects for utilizing its unique genetic features in diverse scientific fields. The present study contributes to the existing literature on Lactiplantibacillus plantarum and sets the stage for prospective investigations and practical implementations that leverage the exceptional genetic characteristics of this adap organism

Assessing the probiotic potential, antioxidant, and antibacterial activities of oat and soy milk fermented with Lactiplantibacillus plantarum strains isolated from Tibetan Kefir

Sufficient intake of probiotics has been shown to help in the digestion, protect the body against pathogenic microorganisms and boost the immune system. Recently, due to high prevalence of milk allergies and lactose intolerance in population, the non-dairy based probiotic alternative are becoming increasing popular. In this context, the oat milk and soya milk-based fermented products can be an ideal alternative for the development of Lactic acid bacteria bacteria based probiotics. These bacteria can not only improve the product’s flavor and bioavailability but also increases its antibacterial and antioxidant capabilities due to fermentation process. The purpose of the resent work was to assess the antioxidant and probiotic properties of oat and soy milk that had been fermented with three different strains of Lactiplantibacillus plantarum (L. plantarum) including L. plantarum 12–3, L. plantarum K25, and L. plantarum YW11 isolated from Tibetan Kefir. Different validated assays were used to evaluate the probiotic properties, adhesion and survival in the digestive system (stomach, acid and bile salts resistance), antioxidant and antimicrobial activities and safety (ABTS and DPPH scavenging assays) of these strains. Results of the study showed that soya milk and oat milk fermented with L. plantarum strains possess promising probiotic, antibacterial and antioxidant properties. These results can be helpful to produce dairy-free probiotic replacements, which are beneficial for those who are unable to consume dairy products due to dietary or allergic restrictions

Molecular docking and density functional theory (DFT) studies on the conversion of linoleic acid into fatty acid metabolites by Lactiplantibacillus plantarum 12-3

The aim of this study was to evaluate the competency of Lactiplantibacillus plantarum 12-3 isolated from Tibetan kefir grains that how it converts linoleic acid (LA) into fatty acid metabolites and what are the main reactions involved in it. Also, we scrutinize the enzymes involved in this study via density functional theory (DFT) and in silico approaches. The taxonomic identity was performed using average nucleotide identity (ANI) analysis and to investigate its genome properties using the rapid annotations using subsystems technology (RAST) annotation service. After eliminating plasmid sequences to focus on core genomic information, ANI analysis was performed using the JSpecies Web Server. The results verified L. plantarum 12-3’s categorization as a member of the L. plantarum species, demonstrating good conservation and taxonomic relatedness. Heatmapper was used to visualize the ANI data clustering and heatmap, allowing the discovery of closely related strains within L. plantarum. RAST annotation of the genome revealed functional subsystems as well as metabolic pathways, cellular activities, and virulence factors. Several routes of future research might be pursued to further investigate the possible applications and distinctive properties of the L. plantarum 12-3 strain. To begin, comparative genomics studies with other L. plantarum strains would provide a better knowledge of the strain’s distinctive genetic variants and evolutionary adaptations. This may give light on its applicability for a variety of industrial uses, including food fermentation and probiotics

Correction: Shabbir et al. Effect of Yeast-Fermented Citrus Pulp as a Protein Source on Nutrient Intake, Digestibility, Nitrogen Balance and In Situ Digestion Kinetics in Nili Ravi Buffalo Bulls. Animals 2021, 11, 1713

Awais Shabbir was mistakenly written as “Muhammad Awais” in the original publication [...

Integrated track of nano-informatics coupling with the enrichment concept in developing a novel nanoparticle targeting ERK protein in Naegleria fowleri

Naegleria fowleri is a free-living amoeba that causes primary amoebic meningoencephalitis. Despite combination drug therapies, N. fowleri is not sensitive to current drug therapies, contributing to the pathogen’s mortality rate of 98%. To enable rational drug designing, this study has proposed an integrated track of nanotechnology coupling with the enrichment concept. In the current study, zinc oxide nanoparticles (ZNP) were screened against ERK protein, which is responsible for the production of pro-inflammatory cytokines that cause brain disturbance in N. fowleri infection. Furthermore, an enrichment analysis has been executed to increase the efficiency of the ZNP through the addition of two amines and one chlorine group. The computational prediction of zeta potential, cytotoxicity, organ toxicity, calculations of binding free energy, and ADMET analysis shows that it is stable and possesses no toxic effect. Amine + chlorine enriched ZNP resulted in a binding energy of −7.8 kcal/mol, a zeta potential reliability of −40 mV, a cytotoxicity of −0.0002, inactive against all the targeted organ models, ADMET profiling shows a molecular weight of 320.54 g/mol, a lipophilicity of −0.99, high water solubility, and good gastrointestinal tract absorption. This proposed invention represents the future work for in vitro in combating this devastating disease toward a reliable therapeutic target with drugs that specifically aimed to inhibit the infection

Artificial Intelligence Assisted Pharmacophore Design for Philadelphia Chromosome-Positive Leukemia with Gamma-Tocotrienol: A Toxicity Comparison Approach with Asciminib

BCR-ABL1 is a fusion protein as a result of a unique chromosomal translocation (producing the so-called Philadelphia chromosome) that serves as a clinical biomarker primarily for chronic myeloid leukemia (CML); the Philadelphia chromosome also occurs, albeit rather rarely, in other types of leukemia. This fusion protein has proven itself to be a promising therapeutic target. Exploiting the natural vitamin E molecule gamma-tocotrienol as a BCR-ABL1 inhibitor with deep learning artificial intelligence (AI) drug design, this study aims to overcome the present toxicity that embodies the currently provided medications for (Ph+) leukemia, especially asciminib. Gamma-tocotrienol was employed in an AI server for drug design to construct three effective de novo drug compounds for the BCR-ABL1 fusion protein. The AIGT’s (Artificial Intelligence Gamma-Tocotrienol) drug-likeliness analysis among the three led to its nomination as a target possibility. The toxicity assessment research comparing AIGT and asciminib demonstrates that AIGT, in addition to being more effective nonetheless, is also hepatoprotective. While almost all CML patients can achieve remission with tyrosine kinase inhibitors (such as asciminib), they are not cured in the strict sense. Hence it is important to develop new avenues to treat CML. We present in this study new formulations of AIGT. The docking of the AIGT with BCR-ABL1 exhibited a binding affinity of −7.486 kcal/mol, highlighting the AIGT’s feasibility as a pharmaceutical option. Since current medical care only exclusively cures a small number of patients of CML with utter toxicity as a pressing consequence, a new possibility to tackle adverse instances is therefore presented in this study by new formulations of natural compounds of vitamin E, gamma-tocotrienol, thoroughly designed by AI. Even though AI-designed AIGT is effective and adequately safe as computed, in vivo testing is mandatory for the verification of the in vitro results

Chain-Engineering-Based De Novo Drug Design against MPXVgp169 Virulent Protein of Monkeypox Virus: A Molecular Modification Approach

The unexpected appearance of the monkeypox virus and the extensive geographic dispersal of cases have prompted researchers to concentrate on potential therapeutic approaches. In addition to its vaccine build techniques, there should be some multiple integrated antiviral active compounds because of the MPV (monkeypox virus) outbreak in 2022. This study offers a computational engineering-based de novo drug discovery mediated by random antiviral active compounds that were screened against the virulent protein MPXVgp169, as one of the key players directing the pathogenesis of the virus. The screening of these candidates was supported by the use of 72 antiviral active compounds. The top candidate with the lowest binding affinity was selected for the engineering of chains or atoms. Literature assisted to identify toxic chains or atoms that were impeding the stability and effectiveness of antiviral compounds to modify them for enhanced efficacy. With a binding affinity of −9.4 Kcal/mol after chain, the lipophilicity of 0.41, the water solubility of 2.51 as soluble, and synthetic accessibility of 6.6, chain-engineered dolutegravir was one of the best active compounds, as proved by the computational engineering analysis. This study will revolutionize the era of drug engineering as a potential therapeutic strategy for monkeypox infection

Design of a novel multiple epitope-based vaccine: An immunoinformatics approach to combat SARS-CoV-2 strains.

From PubMed via Jisc Publications RouterHistory: received 2020-08-16, revised 2021-04-12, accepted 2021-04-22Publication status: aheadofprintSince the SARS-CoV-2 outbreak in December 2019 in Wuhan, China, the virus has infected more than 153 million individuals across the world due to its human-to-human transmission. The USA is the most affected country having more than 32-million cases till date. Sudden high fever, pneumonia and organ failure have been observed in infected individuals. In the current situation of emerging viral disease, there is no specific vaccine, or any therapeutics available for SARS-CoV-2, thus there is a dire need to design a potential vaccine to combat the virus by developing immunity in the population. The purpose of present study was to develop a potential vaccine by targeting B and T-cell epitopes using bioinformatics approaches. B- and T-cell epitopes are predicted from novel M protein-SARS-CoV-2 for the development of a unique multiple epitope vaccine by applying bioinformatics approaches. These epitopes were analyzed and selected for their immunogenicity, antigenicity scores, and toxicity in correspondence to their ability to trigger immune response. In combination to epitopes, best multi-epitope of potential immunogenic property was constructed. The epitopes were joined using EAAAK, AAY and GPGPG linkers. The constructed vaccine showed good results of worldwide population coverage and promising immune response. This constructed vaccine was subjected to in-silico immune simulations by C-ImmSim. Chimeric protein construct was cloned into PET28a (+) vector for expression study in Escherichia coli using snapgene. This vaccine design proved effective in various computer-based immune response analysis as well as showed good population coverage. This study is solely dependent on developing M protein-based vaccine, and these in silico findings would be a breakthrough in the development of an effective vaccine to eradicate SARS-CoV-2 globally. [Abstract copyright: Copyright © 2021 The Authors. Published by Elsevier Ltd.. All rights reserved.

Assessment of the whole genome sequencing of <i>Lactiplantibacillus plantarum</i> 13-3 for elucidation of novel bacteriocin producing gene cluster and confirmation of its potential probiotic functionality and safety applications

Lactiplantibacillus plantarum is a probiotic starter culture that improves the flavor and nutritional content of fermented foods. It also shows potential in enhancing mucosal and systemic immunity, which contributes to overall health. We aimed to examine the complex genetic composition of the L. plantarum 13–3 via a detailed analysis of comparative genomics and our findings discovered that this genome displays high efficacy and conciseness as a nutrition enhancer, encompassing a cumulative sum of 2921 genes encoding proteins and a GC content of 45%. This study clarifies the evolutionary lineage of L. plantarum strains by examining the level of gene order conservation and synteny across various strains. Our strain has been found to possess a range of genetic components, including bacteriocin gene clusters and prophage regions, which indicates its potential applicability in various fields, including biotechnology and medicine. The unique genetic components have the potential to reveal novel therapeutic and biotechnological applications in the future.</p