Primordial soup was edible: abiotically produced Miller-Urey mixture supports bacterial growth.
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ABSTRACT:
SUBMITTER: Xie X
PROVIDER: S-EPMC4585927 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND: The RNA world concept has wide, though certainly not unanimous, support within the origin-of-life scientific community. One view is that life may have emerged as early as the Hadean Eon 4.3-3.8 billion years ago with an atmosphere of high CO(2) producing an acidic ocean of the order of pH 3.5-6. Compatible with this scenario is the intriguing proposal that life arose within alkaline (pH 9-11) deep-sea hydrothermal vents like those of the 'Lost City', with the interface with the acidic ocean creating a proton gradient sufficient to drive the first metabolism. However, RNA is most stable at pH 4-5 and is unstable at alkaline pH, raising the possibility that RNA may have first arisen in the acidic ocean itself (possibly near an acidic hydrothermal vent), acidic volcanic lake or comet pond. As the Hadean Eon progressed, the ocean pH is inferred to have gradually risen to near neutral as atmospheric CO(2) levels decreased. PRESENTATION OF THE HYPOTHESIS: We propose that RNA is well suited for a world evolving at acidic pH. This is supported by the enhanced stability at acidic pH of not only the RNA phosphodiester bond but also of the aminoacyl-(t)RNA and peptide bonds. Examples of in vitro-selected ribozymes with activities at acid pH have recently been documented. The subsequent transition to a DNA genome could have been partly driven by the gradual rise in ocean pH, since DNA has greater stability than RNA at alkaline pH, but not at acidic pH. TESTING THE HYPOTHESIS: We have proposed mechanisms for two key RNA world activities that are compatible with an acidic milieu: (i) non-enzymatic RNA replication of a hemi-protonated cytosine-rich oligonucleotide, and (ii) specific aminoacylation of tRNA/hairpins through triple helix interactions between the helical aminoacyl stem and a single-stranded aminoacylating ribozyme. IMPLICATIONS OF THE HYPOTHESIS: Our hypothesis casts doubt on the hypothesis that RNA evolved in the vicinity of alkaline hydrothermal vents. The ability of RNA to form protonated base pairs and triples at acidic pH suggests that standard base pairing may not have been a dominant requirement of the early RNA world.
| S-EPMC3372908 | biostudies-other
Project description:The effects of different edible fungi on the flavor profiles of fish soups were analyzed by sensory evaluation, non-volatile and volatile flavor compounds. The sensory attributes of fish soups were modified by adding edible fungi, with the highest total scores obtained for AAFS and DFS. Compared with pure fish soup, the amounts of free amino acids, nucleotides, organic acids and inorganic ions were increased with fungi addition, especially AAFS. The different mushroom fish soups could be clearly distinguished by E-nose analysis, and a total of 52 flavor compounds, mainly composed of aldehydes (27), ketones (11), alcohols (8), esters (4), and others (2), were then identified by GC-IMS. Eventually, fish soup samples were classified into three groups based on OPLS-DA analysis: Ⅰ (LEFS), Ⅱ (BFS and BEFS) and Ⅲ (ABFS, AAFS and DFS). The results showed that Agrocybe aegerita had high suitability for improving the flavor of Large yellow croaker soups.
| S-EPMC10825316 | biostudies-literature
Project description:PurposeIn vitro follicle growth (IVFG) is an investigational fertility preservation technique in which immature follicles are grown in culture to produce mature eggs that can ultimately be fertilized. Although progress has been made in growing primate primary and secondary follicles in vitro, it has been a relatively greater challenge to isolate and culture primordial follicles. The purpose of this study was to develop methods to grow human primordial follicles in vitro using alginate hydrogels.MethodsWe obtained human ovarian tissue for research purposes through the National Physicians Cooperative from nationwide sites and used it to test two methods for culturing primordial follicles. First, primordial follicles were isolated from the ovarian cortex and encapsulated in alginate hydrogels. Second, 1 mm × 1 mm pieces of 500 μm-thick human ovarian cortex containing primordial follicles were encapsulated in alginate hydrogels, and survival and follicle development within the tissue was assessed for up to 6 weeks.ResultsWe found that human ovarian tissue could be kept at 4 °C for up to 24 h while still maintaining follicle viability. Primordial follicles isolated from ovarian tissue did not survive culture. However, encapsulation and culture of ovarian cortical pieces supported the survival, differentiation, and growth of primordial and primary follicles. Within several weeks of culture, many of the ovarian tissue pieces had formed a defined surface epithelium and contained growing preantral and antral follicles.ConclusionsThe early stages of in vitro human follicle development require the support of the native ovarian cortex.
| S-EPMC4130945 | biostudies-literature
Project description:Plant growth-promoting rhizobacteria (PGPR) increase plant growth and crop productivity. The inoculation of plants with a bacterial mixture (consortium) apparently provides greater benefits to plant growth than inoculation with a single bacterial strain. In the present work, a bacterial consortium was formulated containing four compatible and desiccation-tolerant strains with potential as PGPR. The formulation had one moderately (Pseudomonas putida KT2440) and three highly desiccation-tolerant (Sphingomonas sp. OF178, Azospirillum brasilense Sp7 and Acinetobacter sp. EMM02) strains. The four bacterial strains were able to adhere to seeds and colonize the rhizosphere of plants when applied in both mono-inoculation and multi-inoculation treatments, showing that they can also coexist without antagonistic effects in association with plants. The effects of the bacterial consortium on the growth of blue maize were evaluated. Seeds inoculated with either individual bacterial strains or the bacterial consortium were subjected to two experimental conditions before sowing: normal hydration or desiccation. In general, inoculation with the bacterial consortium increased the shoot and root dry weight, plant height and plant diameter compared to the non-inoculated control or mono-inoculation treatments. The bacterial consortium formulated in this work had greater benefits for blue maize plants even when the inoculated seeds underwent desiccation stress before germination, making this formulation attractive for future field applications.
| S-EPMC5678714 | biostudies-literature
Project description:Archived samples from a previously unreported 1958 Stanley Miller electric discharge experiment containing hydrogen sulfide (H(2)S) were recently discovered and analyzed using high-performance liquid chromatography and time-of-flight mass spectrometry. We report here the detection and quantification of primary amine-containing compounds in the original sample residues, which were produced via spark discharge using a gaseous mixture of H(2)S, CH(4), NH(3), and CO(2). A total of 23 amino acids and 4 amines, including 7 organosulfur compounds, were detected in these samples. The major amino acids with chiral centers are racemic within the accuracy of the measurements, indicating that they are not contaminants introduced during sample storage. This experiment marks the first synthesis of sulfur amino acids from spark discharge experiments designed to imitate primordial environments. The relative yield of some amino acids, in particular the isomers of aminobutyric acid, are the highest ever found in a spark discharge experiment. The simulated primordial conditions used by Miller may serve as a model for early volcanic plume chemistry and provide insight to the possible roles such plumes may have played in abiotic organic synthesis. Additionally, the overall abundances of the synthesized amino acids in the presence of H(2)S are very similar to the abundances found in some carbonaceous meteorites, suggesting that H(2)S may have played an important role in prebiotic reactions in early solar system environments.
| S-EPMC3078417 | biostudies-literature
Project description:Staphylococcus aureus is a notorious pathogen causing significant morbidity and mortality worldwide. The ability of S. aureus to survive and replicate within phagocytes such as macrophages represents an important facet of immune evasion and contributes to pathogenesis. The mechanisms by which S. aureus acquires nutrients within host cells to support growth remain poorly characterized. Here, we demonstrate that macrophages infected with S. aureus maintain their dynamic ruffling behavior and consume macromolecules from the extracellular milieu. To support the notion that fluid-phase uptake by macrophages can provide S. aureus with nutrients, we utilized the pharmacological inhibitors PIK-III and Dynasore to impair uptake of extracellular macromolecules. Inhibitor treatment also impaired S. aureus replication within macrophages. Finally, using a mutant of S. aureus that is defective in purine biosynthesis we show that intracellular growth is inhibited unless the macrophage culture medium is supplemented with the metabolite inosine monophosphate. This growth rescue can be impaired by inhibition of fluid-phase uptake. In summary, through consumption of the extracellular environment macrophages deliver nutrients to phagolysosomal S. aureus to promote bacterial growth.
| S-EPMC7403714 | biostudies-literature
Project description:IntroductionOne major challenge of reducing salt content in food is the risk of the overall taste becoming bland. Enhancing saltiness is an effective strategy for salt reduction, and the development of salt-reduced foods using these saltiness-enhancing flavorants as food additives is underway. However, an increasing number of consumers demand a reduction in additives in clean-label foods.ObjectiveEnzyme processing of food is an attractive strategy for developing clean-label foods because enzymes are not considered additives. We aimed to improve the saltiness and umami intensity of vegetable soups by enzyme treatment while meeting clean-label requirements. We first optimized the enzymatic reaction conditions of a protease and glutaminase blend and then investigated the synergistic effects of this enzyme blend on the taste of vegetable soup.ResultsSensory evaluations indicated that the reaction products (e.g., protein hydrolysates or amino acids) could enhance the umami, kokumi, and saltiness intensity of vegetable soup supplemented with 0.5% NaCl. Notably, the saltiness intensity ratio of the enzyme-treated soup with 0.50, 0.45, and 0.40% NaCl were increased by 1.31-, 1.16-, and 0.99-fold, respectively, when this ratio for the control soup with 0.50% NaCl was set to 1.0. This indicates a 20% salt reduction rate can be achieved by enzyme treatment. Moreover, we found that these enhancements were synergically caused by enzyme-produced glutamic acid and branched-chain amino acids.ConclusionOur findings suggest that using enzyme blends of bacterial and fungal proteases and glutaminase is an effective approach to enhancing the saltiness levels of vegetable soups while meeting clean-label requirements.
| S-EPMC11368061 | biostudies-literature
Project description:A series of biopolymeric chitosan-based (Ch) films were prepared with choline chloride and citric acid plasticizer (deep eutectic solvent, DES). An effect of adenine (A, vitamin B4) addition on the functional properties of these films was evaluated. Several physicochemical and mechanical properties were tested: Fourier-transformed infrared spectra proved DES's plasticizing and crosslinking effect, while scanning electron microscopy and atomic force microscopy techniques confirmed the possible phase separation after adenine addition. These changes affected the mechanical characteristics and the water vapor and oxygen permeability. The prepared materials are not water soluble because the CA acts as a crosslinker. The adenine addition on antioxidative and antimicrobial properties was also checked. It was found that Ch-DES materials with A exhibit improved antioxidative properties (55.8-66.1% of H2O2 scavenging activity) in contrast to the pristine chitosan-DES material (51.1% of H2O2 scavenging activity), while the material is still non-mutagenic (lack of growth of Salmonella typhimurium) and possesses antimicrobial features (no E. coli observed for all the tested films and inhibition zones noted for S. aureus). The mentioned properties, reduced oxygen transmission (1.6-2.1 g m-2 h-1), and mechanical characteristics within the range of typical food packaging plastics proved the potential of Ch-DES-A films in the packaging sector. Moreover, the antioxidative properties, usage of substrates being allowed as food additives, and the presence of adenine create the advantage of the Ch-DES-A materials as edible coatings, being also a source of Vitamin B4.
| S-EPMC10400631 | biostudies-literature
Project description:When bacterial colonies age most cells enter a stationary phase, but sub-populations of mutant bacteria can continue to grow and accumulate. These sub-populations include bacteria with mutations in rpoB (RNA polymerase β-subunit) or rpoS (RNA polymerase stress-response sigma factor). Here we have identified acetate as a nutrient present in the aging colonies that is utilized by these mutant subpopulations to support their continued growth. Proteome analysis of aging colonies showed that several proteins involved in acetate conversion and utilization were upregulated during aging. Acetate is known to be excreted during the exponential growth phase but can be imported later during the transition to stationary phase and converted to acetyl-CoA. Acetyl-CoA is used in multiple processes, including feeding into the TCA cycle, generating ATP via the glyoxylate shunt, as a source of acetyl groups for protein modification, and to support fatty acid biosynthesis. We showed that deletion of acs (encodes acetyl-CoA synthetase; converts acetate into acetyl-CoA) significantly reduced the accumulation of rpoB and rpoS mutant subpopulations on aging colonies. Measurement of radioactive acetate uptake showed that the rate of conversion decreased in aging wild-type colonies, was maintained at a constant level in the rpoB mutant, and significantly increased in the aging rpoS mutant. Finally, we showed that the growth of subpopulations on aging colonies was greatly enhanced if the aging colony itself was unable to utilize acetate, leaving more acetate available for mutant subpopulations to use. Accordingly, the data show that the accumulation of subpopulations of rpoB and rpoS mutants on aging colonies is supported by the availability in the aging colony of acetate, and by the ability of the subpopulation cells to convert the acetate to acetyl-CoA.
| S-EPMC4183559 | biostudies-literature
Project description:A water-free, ternary solvent mixture consisting of a natural deep eutectic solvent (NADES), ethanol, and triacetin was investigated concerning its ability to dissolve and extract curcumin from Curcuma longa L. To this purpose, 11 NADES based on choline chloride, acetylcholine, and proline were screened using UV-vis measurements. A ternary phase diagram with a particularly promising NADES, based on choline chloride and levulinic acid was recorded and the solubility domains of the monophasic region were examined and correlated with the system's structuring via light scattering experiments. At the optimum composition, close to the critical point, the solubility of curcumin could be enhanced by a factor of >1.5 with respect to acetone. In extraction experiments, conducted at the points of highest solubility and evaluated via HPLC, a total yield of ~84% curcuminoids per rhizome could be reached. Through multiple extraction cycles, reusing the extraction solvent, an enrichment of curcuminoids could be achieved while altering the solution. When counteracting the solvent change, even higher concentrated extracts can be obtained.
| S-EPMC8703436 | biostudies-literature