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Prebiotic information systems exist in three forms: analog, hybrid, and digital. The Analog Information System (AIS), manifested early in abiogenesis, was expressed in the chiral selection, nucleotide formation, self-assembly, polymerization, encapsulation of polymers, and division of protocells. It created noncoding RNAs by polymerizing nucleotides that gave rise to the Hybrid Information System (HIS). The HIS employed different species of noncoding RNAs, such as ribozymes, pre-tRNA and tRNA, ribosomes, and functional enzymes, including bridge peptides, pre-aaRS, and aaRS (aminoacyl-tRNA synthetase). Some of these hybrid components build the translation machinery step-by-step. The HIS ushered in the Digital Information System (DIS), where tRNA molecules become molecular architects for designing mRNAs step-by-step, employing their two distinct genetic codes. First, they created codons of mRNA by the base pair interaction (anticodon–codon mapping). Secondly, each charged tRNA transferred its amino acid information to the corresponding codon (codon–amino acid mapping), facilitated by an aaRS enzyme. With the advent of encoded mRNA molecules, the first genes emerged before DNA. With the genetic memory residing in the digital sequences of mRNA, a mapping mechanism was developed between each codon and its cognate amino acid. As more and more codons ‘remembered’ their respective amino acids, this mapping system developed the genetic code in their memory bank. We compared three kinds of biological information systems with similar types of human-made computer systems.

Information is the currency of life, but the origin of prebiotic information remains a mystery. We propose transitional pathways from the cosmic building blocks of life to the complex prebiotic organic chemistry that led to the origin of information systems. The prebiotic information system, specifically the genetic code, is segregated, linear, and digital, and it appeared before the emergence of DNA. In the peptide/RNA world, lipid membranes randomly encapsulated amino acids, RNA, and peptide molecules, which are drawn from the prebiotic soup, to initiate a molecular symbiosis inside the protocells. This endosymbiosis led to the hierarchical emergence of several requisite components of the translation machine: transfer RNAs (tRNAs), aminoacyl-tRNA synthetase (aaRS), messenger RNAs (mRNAs), ribosomes, and various enzymes. When assembled in the right order, the translation machine created proteins, a process that transferred information from mRNAs to assemble amino acids into polypeptide chains. This was the beginning of the prebiotic information age. The origin of the genetic code is enigmatic; herein, we propose an evolutionary explanation: the demand for a wide range of protein enzymes over peptides in the prebiotic reactions was the main selective pressure for the origin of information-directed protein synthesis. The molecular basis of the genetic code manifests itself in the interaction of aaRS and their cognate tRNAs. In the beginning, aminoacylated ribozymes used amino acids as a cofactor with the help of bridge peptides as a process for selection between amino acids and their cognate codons/anticodons. This process selects amino acids and RNA species for the next steps. The ribozymes would give rise to pre-tRNA and the bridge peptides to pre-aaRS. Later, variants would appear and evolution would produce different but specific aaRS-tRNA-amino acid combinations. Pre-tRNA designed and built pre-mRNA for the storage of information regarding its cognate amino acid. Each pre-mRNA strand became the storage device for the genetic information that encoded the amino acid sequences in triplet nucleotides. As information appeared in the digital languages of the codon within pre-mRNA and mRNA, and the genetic code for protein synthesis evolved, the prebiotic chemistry then became more organized and directional with the emergence of the translation and genetic code. The genetic code developed in three stages that are coincident with the refinement of the translation machines: the GNC code that was developed by the pre-tRNA/pre-aaRS /pre-mRNA machine, SNS code by the tRNA/aaRS/mRNA machine, and finally the universal genetic code by the tRNA/aaRS/mRNA/ribosome machine. We suggest the coevolution of translation machines and the genetic code. The emergence of the translation machines was the beginning of the Darwinian evolution, an interplay between information and its supporting structure. Our hypothesis provides the logical and incremental steps for the origin of the programmed protein synthesis. In order to better understand the prebiotic information system, we converted letter codons into numerical codons in the Universal Genetic Code Table. We have developed a software, called CATI (Codon-Amino Acid-Translator-Imitator), to translate randomly chosen numerical codons into corresponding amino acids and vice versa. This conversion has granted us insight into how the genetic code might have evolved in the peptide/RNA world. There is great potential in the application of numerical codons to bioinformatics, such as barcoding, DNA mining, or DNA fingerprinting. We constructed the likely biochemical pathways for the origin of translation and the genetic code using the Model-View-Controller (MVC) software framework, and the translation machinery step-by-step. While using AnyLogic software, we were able to simulate and visualize the entire evolution of the translation machines, amino acids, and the genetic code.

RationaleThe impact of the microbiota on the gut-brain axis is increasingly appreciated. A growing body of literature demonstrates that use of dietary fibre and prebiotics can manipulate the microbiota and affect host health. However, the influence on cognition and acute stress response is less well understood.ObjectivesThe objective of this study was to investigate the efficacy of a dietary fibre, polydextrose (PDX), in improving cognitive performance and acute stress responses through manipulation of the gut microbiota in a healthy population.MethodsIn this double-blind, randomised, placebo-controlled, crossover design study, 18 healthy female participants received 12.5 g Litesse®Ultra (> 90% PDX polymer) or maltodextrin for 4 weeks. Cognitive performance, mood, acute stress responses, microbiota composition, and inflammatory markers were assessed pre- and post-intervention.ResultsPDX improved cognitive flexibility as evidenced by the decrease in the number of errors made in the Intra-Extra Dimensional Set Shift (IED) task. A better performance in sustained attention was observed through higher number of correct responses and rejections in the Rapid Visual Information Processing (RVP) task. Although there was no change in microbial diversity, abundance of Ruminiclostridium 5 significantly increased after PDX supplementation compared with placebo. PDX supplementation attenuated the increase of adhesion receptor CD62L on classical monocytes observed in the placebo group.ConclusionsSupplementation with the PDX resulted in a modest improvement in cognitive performance. The results indicate that PDX could benefit gut-to-brain communication and modulate behavioural responses.

The ability to encode and convert heritable information into molecular function is a defining feature of life as we know it. The conversion of information into molecular function is performed by the translation process, in which triplets of nucleotides in a nucleic acid polymer (mRNA) encode specific amino acids in a protein polymer that folds into a three-dimensional structure. The folded protein then performs one or more molecular activities, often as one part of a complex and coordinated physiological network. Prebiotic systems, lacking the ability to explicitly translate information between genotype and phenotype, would have depended upon either chemosynthetic pathways to generate its components—constraining its complexity and evolvability— or on the ambivalence of RNA as both carrier of information and of catalytic functions—a possibility which is still supported by a very limited set of catalytic RNAs. Thus, the emergence of translation during early evolutionary history may have allowed life to unmoor from the setting of its origin. The origin of translation machinery also represents an entirely novel and distinct threshold of behavior for which there is no abiotic counterpart—it could be the only known example of computing that emerged naturally at the chemical level. Here we describe translation machinery’s decoding system as the basis of cellular translation’s information-processing capabilities, and the four operation types that find parallels in computer systems engineering that this biological machinery exhibits.

The origin of life remains one of the most profound and enduring enigmas in the biological sciences. Despite substantial advances in prebiotic chemistry, fundamental uncertainties persist regarding the precise mechanisms that enabled the emergence of the first cellular entity and, subsequently, the foundational branches of the tree of life. After examining the core principles that define living systems, we propose that life emerged as a novel property of a prebiotically assembled system—formed through the integration of distinct molecular worlds, defined as sets of structurally and functionally related molecular entities that interact via catalytic, autocatalytic, and/or self-assembly processes. This emergence established a permanent system–process duality, wherein the system’s organization and its dynamic processes became inseparable. Upon acquiring the capacity to replicate and mutate its genetic program, this primordial organism initiated the evolutionary process, ultimately driving the diversification of life under the influence of evolutionary forces and leading to the formation of ecosystems. The challenge of uncovering the origin of life and the emergence of biodiversity is not solely scientific, it requires the integration of empirical evidence, theoretical insight, and critical reflection. This work does not claim certainty but proposes a perspective on how life and biodiversity may have arisen on Earth. Ultimately, time and scientific inquiry will determine the validity of this view.

Background There is wide agreement that only a subset of the twenty standard amino acids existed prebiotically in sufficient concentrations to form functional polypeptides. We ask how this subset, postulated as {A,D,E,G,I,L,P,S,T,V}, could have formed structures stable enough to found metabolic pathways. Inspired by alphabet reduction experiments, we undertook a computational analysis to measure the structural coding behavior of sequences simplified by reduced alphabets. We sought to discern characteristics of the prebiotic set that would endow it with unique properties relevant to structure, stability, and folding. Results Drawing on a large dataset of single-domain proteins, we employed an information-theoretic measure to assess how well the prebiotic amino acid set preserves fold information against all other possible ten-amino acid sets. An extensive virtual mutagenesis procedure revealed that the prebiotic set excellently preserves sequence-dependent information regarding both backbone conformation and tertiary contact matrix of proteins. We observed that information retention is fold-class dependent: the prebiotic set sufficiently encodes the structure space of α/β and α + β folds, and to a lesser extent, of all-α and all-β folds. The prebiotic set appeared insufficient to encode the small proteins. Assessing how well the prebiotic set discriminates native vs. incorrect sequence-structure matches, we found that α/β and α + β folds exhibit more pronounced energy gaps with the prebiotic set than with nearly all alternatives. Conclusions The prebiotic set optimally encodes local backbone structures that appear in the folded environment and near-optimally encodes the tertiary contact matrix of extant proteins. The fold-class-specific patterns observed from our structural analysis confirm the postulated timeline of fold appearance in proteogenesis derived from proteomic sequence analyses. Polypeptides arising in a prebiotic environment will likely form α/β and α + β-like folds if any at all. We infer that the progressive expansion of the alphabet allowed the increased conformational stability and functional specificity of later folds, including all-α, all-β, and small proteins. Our results suggest that prebiotic sequences are amenable to mutations that significantly lower native conformational energies and increase discrimination amidst incorrect folds. This property may have assisted the genesis of functional proto-enzymes prior to the expansion of the full amino acid alphabet.

According to Information Vortex Theory, the spatially distributed wave energy associated with the constituent molecules of an incepting cell interacts with the surrounding space to generate a rotating bioinformation field, forming a vortex. This vortex, characterized as a local maximum of energy density, constitutes both inbound and outbound energy fluxes, corresponding to signal reception and dispersal, respectively. The vortex represents a foundational step in the emergence of life, facilitating both the storage of information and, through successive wave superpositions, the basic processing of information. This mechanism is posited to underpin the self-organizing principles that are essential to life's origin. This study delineates the sequence of events within the information vortex that are causative to the emergence of plant life, emphasizing the role of a central information processing means, which determines evolutionary steps. An environmental context that resists cytoplasmic motion leads to signals favoring pinocytosis, which progressively intensify within the emerging information vortex while concurrently diminishing the expression of phagocytic wave forms. Furthermore, asexual reproductive events, represented by self-division waveforms, propagate this encoded information across successive generations. To elucidate these mechanisms, system-level modeling incorporating feedback loops and adaptive interventions is developed, illustrating the iterative nature of learning and pattern reinforcement. In parallel, a wave-theory-based mathematical framework is introduced to characterize the information vortex energy fluxes and the encoding of the arriving signals epigenetically in the genome.

Objective: In the present research work, we examined the dietary Moringa oleifera effect on gut health and growth traits in chickens. Materials and Methods: There were 280 chicks (day old) that were weighted and allotted uni¬formly in seven groupings, each containing eight replicates (n = 5). Birds were supplemented with M. oleifera leaf extract (MLE) and seed extract (MSE) for 35 days. Group I was the control (fed merely basal diets), while Group II received 0.8% MLE, Group III was given 0.8% MSE, Group IV was given 1.2% MLE, Group V was given 1.2% MSE, Group VI was given 0.8% MLE + 0.8% MSE, and Group VII was given 1.2% MLE + 1.2% MSE. At the end of the fifth week, two chickens were selected from each replica, and samples (small intestine and ileal ingesta) were collected. Results: The chicken diet with MLE and MSE supplements saw significant improvement (p < 0.05) in both feed conversion ratio (FCR) and body weight gain (BWG). In the small intestine (duodenal, jejunal, and ileal), dietary MLE and MSE supplements significantly increased (p < 0.05) the surface area of the villus and the ratio of their height/crypt depth in comparison to the control group. The MLE and MSE supplements significantly increased (p < 0.05) the total goblet cell counts in the small intestine. The Lactobacillus spp. count was significantly improved (p < 0.05) and reduced (p < 0.05) in Escherichia coli counts when the bird diet was supplemented with MLE (0.8%) and MSE (0.8%). Conclusion: Results indicated that M. oleifera leaf and seed extract diet improved the growth trait and gut health in chickens.

A crucial stage in the origin of life was the emergence of the first molecular entity that was able to replicate, transmit information, and evolve on the early Earth. The amyloid world hypothesis posits that in the pre-RNA era, information processing was based on catalytic amyloids. The self-assembly of short peptides into β-sheet amyloid conformers leads to extraordinary structural stability and novel multifunctionality that cannot be achieved by the corresponding nonaggregated peptides. The new functions include self-replication, catalytic activities, and information transfer. The environmentally sensitive template-assisted replication cycles generate a variety of amyloid polymorphs on which evolutive forces can act, and the fibrillar assemblies can serve as scaffolds for the amyloids themselves and for ribonucleotides proteins and lipids. The role of amyloid in the putative transition process from an amyloid world to an amyloid–RNA–protein world is not limited to scaffolding and protection: the interactions between amyloid, RNA, and protein are both complex and cooperative, and the amyloid assemblages can function as protometabolic entities catalyzing the formation of simple metabolite precursors. The emergence of a pristine amyloid-based in-put sensitive, chiroselective, and error correcting information-processing system, and the evolvement of mutualistic networks were, arguably, of essential importance in the dynamic processes that led to increased complexity, organization, compartmentalization, and, eventually, the origin of life.

Background: Postbiotics are bioactive compounds derived from inactivated probiotic microorganisms that show potential for preventing and treating inflammatory diseases. This review aimed to evaluate the evidence on their therapeutic effects in inflammatory conditions. Methods: A search of PubMed, Scopus, and Web of Science databases from 2014 to 2024 identified 39 eligible studies. Article selection was conducted using the Rayyan platform, risk of bias was assessed with the Cochrane ROB 2 tool, and results were visualized with ROBVIS. Bibliometric networks were constructed using VOSviewer. Due to data heterogeneity, a meta-analysis was not performed; therefore, results were described and presented graphically. Results: The most commonly used microorganisms belonged to the Lactobacillaceae and Bifidobacteriaceae families, with heat inactivation as the predominant method. Postbiotics exert multifaceted anti-inflammatory effects by modulating cytokine expression, influencing immune cell signaling pathways, and strengthening epithelial barrier integrity. They regulate immune mechanisms such as the Th1/Th2 and Treg/Th17 balance, indicating their potential in treating inflammatory bowel diseases, autoimmune diseases, and metabolic syndrome. However, the heterogeneity of studies, their limitations, and risk of bias require cautious interpretation. Conclusions: Future research should focus on standardizing postbiotic preparations, conducting long-term clinical trials, and analyzing synergistic effects of different strains. Postbiotics offer a promising approach to managing inflammation, with potential applications in functional foods and nutraceuticals.