Search Results (43)

Background/Objectives: Correction of decreased diversity of the gut microbiome, which is characteristic of menopause, by supplementation with a synbiotic may attenuate or prevent dysbiosis processes and preserve bone mass. We describe the rationale and design of the OsteoPreP trial aimed at evaluating the effects of 12 months of supplementation with a synbiotic on bone and metabolic health in postmenopausal Caucasian women. Methods: This is a randomized, double-blinded, placebo-controlled trial among 160 Caucasian, postmenopausal women with no current diagnosis of osteoporosis or supplementation with pro- or prebiotics, and no medical treatment affecting bone turnover. Dual-energy X-ray absorptiometry scans will be conducted at screening to confirm absence of osteoporosis. The primary outcome is the relative change (%) in total bone mineral density of the distal tibia at 12 months post-treatment between the active and placebo groups, as determined via high-resolution peripheral quantitative computed tomography. Secondary outcomes are the effects on immune system modulation and cognition, gut microbiota composition, and musculoskeletal and metabolic functions, with particular emphasis on blood glucose regulation. Conclusions: The trial will inform on the efficacy and safety of a synbiotic containing both aerobic and anerobic bacterial strains and a prebiotic fiber on reduction in bone loss and on indices of blood glucose regulation. This trial may pave the way for an exciting field of translational research and be the underpinnings of the prevention strategy of osteoporosis and the management of metabolic dysfunction in postmenopausal women. The trial is registered with clinicaltrials.gov (NCT05348694). Full article

Glycogen is a highly branched polyglucan utilized as a carbohydrate reserve in major living systems. Industrially, it is used as a prebiotic and in the nanoencapsulation of drugs and nutraceuticals. In this study, optimal fermentation conditions enabling the highest glycogen accumulation in Saccharomyces cerevisiae were experimentally evaluated for possible mass production. Production efficiency was assessed by comparing specific growth rates, specific glycogen production rates, and glycogen yields under each condition. The results demonstrated that fermentation at 30 °C with an aeration rate of 3 vvm using a medium containing 120 g/L glucose without ethanol was optimal for robust cell growth and maximum glycogen yield. Additionally, a rich medium outperformed a minimally defined medium, and a single sugar carbon source, as opposed to mixed sugars, resulted in significantly higher cell growth and glycogen yields (p < 0.05). The optimized fermentation parameters enabled a glycogen production rate of up to 0.232 ± 0.012 g-glycogen/g-cell/h and a glycogen yield of 0.603 ± 0.006 g-glycogen/g-glucose. These results provide meaningful information for future studies and/or large-scale glycogen production using S. cerevisiae. Full article

Prebiotic pre-Darwinian reactions continued throughout biochemical or Darwinian evolution. Early chemical processes could have occurred on Earth between 4.5 and 3.6 billion years ago when cellular life was about to come into being. Pre-Darwinian evolution assumes the development of hereditary elements but does not regard them as self-organizing processes. The presence of biochemical self-organization after the pre-Darwinian evolution did not justify distinguishing between different types of evolution. From the many possible solutions, evolution selected from among those stable reactions that led to catalytic networks, and under gradually changing external conditions produced a reproducible, yet constantly evolving and adaptable, living system. Major abiotic factors included sunlight, precipitation, air, minerals, soil and the Earth’s atmosphere, hydrosphere and lithosphere. Abiotic sources of chemicals contributed to the formation of prebiotic RNA, the development of genetic RNA, the RNA World and the initial life forms on Earth and the transition of genRNA to the DNA Empire, and eventually to the multitude of life forms today. The transition from the RNA World to the DNA Empire generated new processes such as oxygenic photosynthesis and the hierarchical arrangement of processes involved in the transfer of genetic information. The objective of this work is to unite earlier work dealing with the formose, the origin and synthesis of ribose and RNA reactions that were published as a series of independent reactions. These reactions are now regarded as the first metabolic pathway. Full article

The evolution of the translation system is a fundamental issue in the quest for the origin of life. A feasible evolutionary scenario necessitates the autonomous emergence of a protoribosome capable of catalyzing the synthesis of the initial peptides. The peptidyl transferase center (PTC) region in the modern ribosomal large subunit is believed to retain a vestige of such a prebiotic non-coded protoribosome, which would have self-assembled from random RNA chains, catalyzed peptide bond formation between arbitrary amino acids, and produced short peptides. Recently, three research groups experimentally demonstrated that several distinct dimeric constructs of protoribosome analogues, derived predicated on the approximate 2-fold rotational symmetry inherent in the PTC region, possess the ability to spontaneously fold, dimerize, and catalyze the formation of peptide bonds and of short peptides. These dimers are examined, aiming at retrieving information concerned with the characteristics of a prebiotic protoribosome. The analysis suggests preconditions for the laboratory re-creation of credible protoribosome analogues, including the preference of a heterodimer protoribosome, contradicting the common belief in the precedence of homodimers. Additionally, it derives a dynamic process which possibly played a role in the spontaneous production of the first bio-catalyzed peptides in the prebiotic world. Full article

To understand the origins of life, we must first gain a grasp of the unresolved emergence of the first informational polymers and cell-like assemblies that developed into living systems. Heating amino acid mixtures to their boiling point produces thermal proteins that self-assemble into membrane-bound protocells, offering a compelling abiogenic route for forming polypeptides. Recent research has revealed the presence of electrical excitability and signal processing capacities in proteinoids, indicating the possibility of primitive cognitive functions and problem-solving capabilities. This review examines the characteristics exhibited by proteinoids, including electrical activity and self-assembly properties, exploring the possible roles of such polypeptides under prebiotic conditions in the emergence of early biomolecular complexity. Experiments showcasing the possibility of unconventional computing with proteinoids as well as modelling proteinoid assemblies into synthetic proto-brains are given. Proteinoids’ robust abiogenic production, biomimetic features, and computational capability shed light on potential phases in the evolution of polypeptides and primitive life from the primordial environment. Full article

The origin of genetic coding is characterised as an event of cosmic significance in which quantum mechanical causation was transcended by constructive computation. Computational causation entered the physico-chemical processes of the pre-biotic world by the incidental satisfaction of a condition of reflexivity between polymer sequence information and system elements able to facilitate their own production through translation of that information. This event, which has previously been modelled in the dynamics of Gene–Replication–Translation systems, is properly described as a process of self-guided self-organisation. The spontaneous emergence of a primordial genetic code between two-letter alphabets of nucleotide triplets and amino acids is easily possible, starting with random peptide synthesis that is RNA-sequence-dependent. The evident self-organising mechanism is the simultaneous quasi-species bifurcation of the populations of information-carrying genes and enzymes with aminoacyl-tRNA synthetase-like activities. This mechanism allowed the code to evolve very rapidly to the ~20 amino acid limit apparent for the reflexive differentiation of amino acid properties using protein catalysts. The self-organisation of semantics in this domain of physical chemistry conferred on emergent molecular biology exquisite computational control over the nanoscopic events needed for its self-construction. Full article

The Braess paradox (discovered in 1968 by the German mathematician Dietrich Braess) describes how a possible relief of a system, by introducing new possibilities to distribute load or local density in flows inside the system, can actually increase stress on the system. It is most often researched in a world of rational decision-makers, who are assumed to cause the worsening situation due to rational optimization of individual interests. In strongly complex networks, the exploitation of new possibilities most probably needs rational decision-makers who can see the use of new possibilities for them. Interestingly, a mechanical analogy of the situation also exists, where new possibilities—in this case for forces in a system to attack—lead to a loss of stability inside the system. In this example, a string that was introduced to relieve the load on two springs leads to counter-intuitive overloading. With the perspective that the evolution of information processing systems is already beginning in a physical and chemical pre-biotic world, this is an interesting case that might give further insight into how and when choices between many possibilities could threaten the function of a system rather than making it more durable and adaptable. The example is discussed based on a review of literature from the humanities as well as the natural sciences. Full article

The origin of life possibly required processes in confined systems that facilitated simple chemical reactions and other more complex reactions impossible to achieve under the condition of infinite dilution. In this context, the self-assembly of micelles or vesicles derived from prebiotic amphiphilic molecules is a cornerstone in the chemical evolution pathway. A prime example of these building blocks is decanoic acid, a short-chain fatty acid capable of self-assembling under ambient conditions. This study explored a simplified system made of decanoic acids under temperatures ranging from 0 °C to 110 °C to replicate prebiotic conditions. The study revealed the first point of aggregation of decanoic acid into vesicles and examined the insertion of a prebiotic-like peptide in a primitive bilayer. The information gathered from this research provides critical insights into molecule interactions with primitive membranes, allowing us to understand the first nanometric compartments needed to trigger further reactions that were essential for the origin of life. Full article

Walnuts have been lauded as a ‘superfood’, containing a remarkable array of natural constituents that may have additive and/or synergistic properties that contribute to reduced cancer risk. Walnuts are a rich source of polyunsaturated fatty acids (PUFAs: alpha-linolenic acid, ALA), tocopherols, antioxidant polyphenols (including ellagitannins), and prebiotics, including fiber (2 g/oz). There is a growing body of evidence that walnuts may contribute in a positive way to the gut microbiome, having a prebiotic potential that promotes the growth of beneficial bacteria. Studies supporting this microbiome-modifying potential include both preclinical cancer models as well as several promising human clinical trials. Mediated both directly and indirectly via its actions on the microbiome, many of the beneficial properties of walnuts are related to a range of anti-inflammatory properties, including powerful effects on the immune system. Among the most potent constituents of walnuts are the ellagitannins, primarily pedunculagin. After ingestion, the ellagitannins are hydrolyzed at low pH to release ellagic acid (EA), a non-flavonoid polyphenolic that is subsequently metabolized by the microbiota to the bioactive urolithins (hydroxydibenzo[b,d]pyran-6-ones). Several urolithins, including urolithin A, reportedly have potent anti-inflammatory properties. These properties of walnuts provide the rationale for including this tree nut as part of a healthy diet for reducing overall disease risk, including colorectal cancer. This review considers the latest information regarding the potential anti-cancer and antioxidant properties of walnuts and how they may be incorporated into the diet to provide additional health benefits. Full article

Extant biology uses RNA to record genetic information and proteins to execute biochemical functions. Nucleotides are translated into amino acids via transfer RNA in the central dogma. tRNA is essential in translation as it connects the codon and the cognate amino acid. To reveal how the translation emerged in the prebiotic context, we start with the structure and dissection of tRNA, followed by the theory and hypothesis of tRNA and amino acid recognition. Last, we review how amino acids assemble on the tRNA and further form peptides. Understanding the origin of life will also promote our knowledge of artificial living systems. Full article

Prebiotics and probiotics have gained much attention in the pursuit of a healthy life. Recently, postbiotics have been spotlighted as next-generation compounds that can improve health. Postbiotics are designated into non-viable, inactivated, and ghost probiotics, and linked to several health benefits for the gut, immune system, and various other aspects of health. This study investigated the anti-proliferation effects of postbiotics against HT-29 cells, a colon cancer cell line. The postbiotics were produced by the ultrasonication method from two Lactobacillus strains (Lactobacillus sp. La1, and La2) and designated to Pobt-La1 and Pobt-La2, respectively, and non-viability was confirmed on the plate media. The anti-proliferation effect was concentration-dependent. The HT-29 cells showed viabilities of 39% and 49% when treated with 300 µL/mL of Pobt-La1 and Pobt-La2, respectively. During observation of the morphological changes of HT-29 cells when treated with IC50, a cell nucleus was not observed but cell condensation was observed. Moreover, in comparison with the control group, a reduced number of cells were observed. Based on these results, it considered that the postbiotic compounds from Lactobacillus La1 and La2 could provide crucial information in the development of anticancer research. Through further research, it would be beneficial to investigate the possibility of using these postbiotics (Pobt-La1 and -La2) as an anticancer drug. Full article

Honey bees and honey, have been the subject of study for decades due to their importance in improving health. At times, some of the probiotics may be transferred to the honey stored in the honeycomb. Consumers may benefit from consuming live-probiotics honey, which can aid in suppressing the reproduction of pathogens in their digestive system. Prebiotics, on the other hand, are mainly carbohydrates that promote the growth of native microflora probiotics in the digestive tract to maintain a healthy environment and improve the gut performance of the host. Therefore, this narrative review aims to present and analyze ten years’ worth of information on the probiotic and prebiotic potential of honey bees and honey since not many review articles were found discussing this topic. Results showed that not many studies have been performed on the probiotic and prebiotic aspects of honey bees and honey. If further research is conducted, isolated probiotics from the bee’s gut combined with honey’s prebiotic properties can be manipulated as potential sources of probiotics and prebiotics for human and animal benefits since they appear to be interrelated and function in symbiosis. Full article

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. Full article

The gut of warm-blooded animals is colonized by microbes possibly constituting at least 100 times more genetic material of microbial cells than that of the somatic cells of the host. These microbes have a profound effect on several physiological functions ranging from energy metabolism to the immune response of the host, particularly those associated with the gut immune system. The gut of a newly hatched chick is typically sterile but is rapidly colonized by microbes in the environment, undergoing cycles of development. Several factors such as diet, region of the gastrointestinal tract, housing, environment, and genetics can influence the microbial composition of an individual bird and can confer a distinctive microbiome signature to the individual bird. The microbial composition can be modified by the supplementation of probiotics, prebiotics, or synbiotics. Supplementing these additives can prevent dysbiosis caused by stress factors such as infection, heat stress, and toxins that cause dysbiosis. The mechanism of action and beneficial effects of probiotics vary depending on the strains used. However, it is difficult to establish a relationship between the gut microbiome and host health and productivity due to high variability between flocks due to environmental, nutritional, and host factors. This review compiles information on the gut microbiota, dysbiosis, and additives such as probiotics, postbiotics, prebiotics, and synbiotics, which are capable of modifying gut microbiota and elaborates on the interaction of these additives with chicken gut commensals, immune system, and their consequent effects on health and productivity. Factors to be considered and the unexplored potential of genetic engineering of poultry probiotics in addressing public health concerns and zoonosis associated with the poultry industry are discussed. Full article

The RNA world is one of the principal hypotheses to explain the emergence of living systems on the prebiotic Earth. It posits that RNA oligonucleotides acted as both carriers of information as well as catalytic molecules, promoting their own replication. However, it does not explain the origin of the catalytic RNA molecules. How could the transition from a pre-RNA to an RNA world occur? A starting point to answer this question is to analyze the dynamics in sequence space on the lowest level, where mononucleotide and short oligonucleotides come together and collectively evolve into larger molecules. To this end, we study the sequence-dependent self-assembly of polymers from a random initial pool of short building blocks via templated ligation. Templated ligation requires two strands that are hybridized adjacently on a third strand. The thermodynamic stability of such a configuration crucially depends on the sequence context and, therefore, significantly influences the ligation probability. However, the sequence context also has a kinetic effect, since non-complementary nucleotide pairs in the vicinity of the ligation site stall the ligation reaction. These sequence-dependent thermodynamic and kinetic effects are explicitly included in our stochastic model. Using this model, we investigate the system-level dynamics inside a non-equilibrium ‘RNA reactor’ enabling a fast chemical activation of the termini of interacting oligomers. Moreover, the RNA reactor subjects the oligomer pool to periodic temperature changes inducing the reshuffling of the system. The binding stability of strands typically grows with the number of complementary nucleotides forming the hybridization site. While shorter strands unbind spontaneously during the cold phase, larger complexes only disassemble during the temperature peaks. Inside the RNA reactor, strand growth is balanced by cleavage via hydrolysis, such that the oligomer pool eventually reaches a non-equilibrium stationary state characterized by its length and sequence distribution. How do motif-dependent energy and stalling parameters affect the sequence composition of the pool of long strands? As a critical factor for self-enhancing sequence selection, we identify kinetic stalling due to non-complementary base pairs at the ligation site. Kinetic stalling enables cascades of self-amplification that result in a strong reduction of occupied states in sequence space. Moreover, we discuss the significance of the symmetry breaking for the transition from a pre-RNA to an RNA world. Full article