attempted prebiotic synthesis of pseudouridine

Pseudouridine is a modified base found in all tRNA and rRNA. Hence, it is reasonable to think that pseudouridine was important in the early evolution, if not the origin, of life. Since uracil reacts rapidly with formaldehyde and other aldehydes at the C-5 position, it is plausible that pseudouridine could be synthesized in a similar way by the reaction of the C-5 of uracil with the C-1 of ribose. The determining factor is whether the ribose could react with the uracil faster than ribose decomposes. However, both rates are determined by the amount of free aldehyde in the ribose. Various plausible prebiotic reactions were investigated and none showed pseudouridine above the detection limit (<0.01%). Only unreacted uracil and ribose decomposition products could be observed. Thus the rate of addition of ribose to uracil is much slower than the decomposition of ribose under any reasonable prebiotic conditions. Unless efficient non-biological catalysts for any of these reactions exist, pseudouridine would not have been synthesized to any significant extent without the use of biologically produced enzymes.     

Prebiotic ribose synthesis: A critical analysis

The discovery of catalytic ability in RNA has given fresh impetus to speculations that RNA played a critical role in the origin of life. This question must rest on the plausibility of prebiotic oligonucleotide synthesis, rather than on the properties of the final product. Many cliams have been published to support the idea that the components of RNA were readily available on the prebiotic earth. In this article, the literature cited in support of the prebiotic availability of one subunit, D-ribose, is reviewed to determine whether it justifies the claim.Polymerization of formaldehyde (the formose reaction) has been the single reaction cited for prebiotic ribose synthesis. It has been conducted with different catalysts: numerous basic substances, neutral clays and heat, and various types of radiation. Ribose has been identified (yields are uncertain, but unlikely to be greater than 1%) in reactions run with concentrated (0.15 M or greater) formaldehyde. It has been claimed in reactions run at lower concentration, but characterization has been inadequate, and experimental details have not been provided.The complex sugar mixture produced in the formose reaction is rapidly destroyed under the reaction conditions. Nitrogenous substances (needed for prebiotic base synthesis) would interfere with the formose reaction by reacting with formaldehyde, the intermediates, and sugar products in undesirable ways.The evidence that is currently available does not support the availability of ribose on the prebiotic earth, except perhaps for brief periods of time, in low concentration as part of a complex mixture, and under conditions unsuitable for nucleoside synthesis.     

The prebiotic synthesis of carbohydrates: A reassessment

Summary Questions concerning the significance of previous work on the formose reaction have led us to reexamine the question of the prebiotic synthesis of sugars. The results of new experiments lead to the following conclusions: The formose reaction is a geochemically plausible reaction which depends on neither basic conditions nor on the presence of trace amounts of carbohydrate impurities. However, this process is not a plausible source of ribose nor of any other individual sugar. In contrast to the nonspecific formation of complex mixtures of sugars via the formose reaction, the reduced sugar pentaerythritol is formed with great selectivity by the ultraviolet irradiation of 0.1 M formaldehyde. This compound may have played an important role in chemical evolution.Offprint requests to: A.W. Schwartz     

Separation of saccharides derivatized with 2-aminobenzoic acid by capillary electrophoresis and their structural consideration by nuclear magnetic resonance

Saccharides including mono- and disaccharides were quantitatively derivatized with 2-aminobenzoic acid (2-AA). These derivatives were then separated by capillary zone electrophoresis with UV detection using 50mM sodium phosphate buffer as the running electrolyte solution. In particular, the saccharide derivatives with the same molecular weight as 2-AA aldohexoses (mannose and glucose) and 2-AA aldopentoses (ribose and xylose) were well separated. The underlying reasons for separation were explored by studying their structural data using 1H and 13C NMR. It was found that the configurational difference between their hydroxyl group at C2 or C3 could cause the difference in Stokes' radii between their molecules and thus lead to different electrophoretic mobilities. The correlation between the electrophoretic behavior of these carbohydrate derivatives and their structures was studied utilizing the calculated molecular models of the 2-AA-labeled mannose, glucose, ribose, and xylose.     

The influence of prebiotic-type organic molecules on the crystallization of Al and Mg hydroxides

It is now well accepted that clays could have concentrated prebiotic organic molecules, protected them from UV radiation, and served as templates and catalysts in their prebiotic evolution. A complementary question is: How did prebiotic organics in the oceans, in ground water, or in hydrothermal solutions affect the formation and inorganic evolution of oxides, hydroxides, and clay minerals? In this study predominantly amorphous Al oxyhydroxides (Al gels) and crystalline Mg hydroxyoxides were synthesized, and then crystallized and recrystallized respectively, to Al and Mg hydroxides via wet and dry (w/d) cycling using both water and organic solutions. The products that resulted were examined using IR spectroscopy and X-ray diffraction (XRD). XRD scans of the products formed by w/d cycling of the Al gels with either water or 0.1 M aqueous solutions of methanol or formaldehyde showed that bayerite (α Al₂O₃) was the major phase formed. The acetonitrile treated sample exhibited the most defined XRD peaks, and no crystalline phase could be observed by XRD of the 0.1 M formamide solution treated sample. Cycling the Mg hydroxyoxide with water, or 0.1 M solutions of methanol, formamide, formaldehyde, or acetonitrile resulted in the formation of brucite (Mg(OH)₂) (in varying amounts) and of three unidentified phases. One unidentified phase, ‘phase II’, was observed in the formaldehyde cycled sample (and tentatively identified in the methanol and formamide cycled samples), ‘phase III’ in the formamide and formaldehyde cycled sample, and ‘phase IV’ in only the formaldehyde. XRD peaks with a spacing of approximately 11.5 Å (assigned to phase III) suggest intercalation of formamide and formaldehyde into the interlayer spaces of the brucite. Phosphate treatment, prior to w/d cycling with water, and also with the above mentioned organics, while totally preventing subsequent formation of any crystalline Al hydroxide, enhanced the formation of Mg phases, shown by XRD data. Formation of brucite was impeded only by w/d cycling using concentrated methanol solution, but even these effects were reversible. The XRD scans of the products resulting from the aqueous and organic solution cycling treatments of the Mg starting materials showed peaks due to brucite and three unidentified phases. Only the brucite is evident in oriented sample XRD scans of the Mg starting material when treated with methanol, formamide, and acetonitrile. In random powder sample XRD scans of the Mg starting material treated with: 1) methanol — the unidentified phase II is evident, 2) formamide — phase II and III are seen, and 3) formaldehyde — phases II, III, and IV are evident.     

Nucleotide analogs based on pentaerythritol — An hypothesis

The synthesis of ribose and ribose-based nucleotides under reasonable prebiotic conditions has not been achieved. Glycerol has been suggested as a structural unit that might have preceded ribose in the evolutionary emergence of RNA. Template-directed oligomerizations of nucleotide analogs based on glycerol, however, have been only partially successful. Recent studies on the effect of ultraviolet irradiation of formaldehyde solutions have shown that the reduced sugar pentaerythritol is formed with great specificity. I argue that pentaerythritol is potentially capable of being converted by simple chemistry into a series of nucleoside analogs related to barbituric acid. These analogs may be able to take part in nucleic acid-like interactions and could therefore be of potential interest as a new class of candidates as RNA precursors.     

Plausible prebiotic synthesis of aldopentoses from simple substrates, glycolaldehyde and formaldehyde

Possible ways of abiotic catalytic synthesis of biologically significant aldopentoses (ribose, xylose, arabinose, lyxose) from elementary substrates, i.e., formaldehyde (FA) and glycolaldehyde (GA) in aqueous solutions are discussed. Conditions in which the process of synthesis of pentoses yields up to 65% relative to the initial concentration of GA: homogeneous borate catalyst NaOH + H₃BO₃, pH 9, [GA]₀ 5 mM, [FA]₀ 50–100 mM have been found.     

Is Boron a Prebiotic Element? A Mini-review of the Essentiality of Boron for the Appearance of Life on Earth

Boron is probably a prebiotic element with special importance in the so-called "sugars world". Boron is not present on Earth in its elemental form. It is found only in compounds, e.g., borax, boric acid, kernite, ulexite, colemanite and other borates. Volcanic spring waters sometimes contain boron-based acids (e.g., boric, metaboric, tetraboric and pyroboric acid). Borates influence the formation of ribofuranose from formaldehyde that feeds the "prebiotic metabolic cycle". The importance of boron in the living world is strongly related to its implications in the prebiotic origins of genetic material; consequently, we believe that throughout the evolution of life, the primary role of boron has been to provide thermal and chemical stability in hostile environments. The complexation of boric acid and borates with organic cis-diols remains the most probable chemical mechanism for the role of this element in the evolution of the living world. Because borates can stabilize ribose and form borate ester nucleotides, boron may have provided an essential contribution to the "pre-RNA world".     

On the Ability of Formaldehyde to Act as a Tethering Catalyst in Water

The low concentration issue is a fundamental challenge when it comes to prebiotic chemistry, as macromolecular systems need to be assembled via intermolecular reactions, and this is inherently difficult in dilute solutions. This is especially true when the reactions are challenging, and reactions that proceeded more rapidly could have dictated chemical evolution. Herein we establish that formaldehyde is capable of catalyzing, via temporary intramolecularity, a challenging reaction in water at low concentrations, thus providing an alternative to other approaches that can either lead to higher concentrations or higher effective molarities.     

Boron Enrichment in Martian Clay

We have detected a concentration of boron in martian clay far in excess of that in any previously reported extra-terrestrial object. This enrichment indicates that the chemistry necessary for the formation of ribose, a key component of RNA, could have existed on Mars since the formation of early clay deposits, contemporary to the emergence of life on Earth. Given the greater similarity of Earth and Mars early in their geological history, and the extensive disruption of Earth''s earliest mineralogy by plate tectonics, we suggest that the conditions for prebiotic ribose synthesis may be better understood by further Mars exploration.     

Boronic acid mono- and diesters of the aldopentoses

The four aldopentoses ribose, arabinose, xylose, and lyxose were evaluated to test their suitability as linear linkers for the formation of intrinsically chiral covalent organic boronic ester networks. Based on X-ray crystal structures of the reaction products with phenylboronic acid, arabinose and xylose formed boronic acid diesters. Lyxose and ribose formed monoesters under the conditions employed. NMR shielding constants were calculated by DFT methods. The results are highly correlated with the experimentally observed NMR shift values.     

A Possible Path to the RNA World: Enantioselective and Diastereoselective Purification of Ribose

A theoretical mechanism resulting in the prebiotic appearance of enantiopure ribose, which would be needed for the origin of RNA and the “RNA world” is proposed. The mechanism simultaneously explains the emergence of biological homochirality and could answer the question of why nucleic acids are based on ribose rather than another sugar. Cleavage of certain non-chiral mineral crystals is known to lead to formation of chiral surfaces. In a chromatography-like process a mixture of racemic carbohydrates originating from the formose reaction is proposed to have been separated on such a chiral surface. Monosaccharides interact with surfaces through their hydroxyl groups, either by hydrogen bond formation or complex formation with metal ions. α-Ribopyranose, which has all hydroxyl groups on one side of the ring, is known to interact more strongly than other sugars with surfaces, as corroborated by certain chromatographic and electrophoresis data. A similar scenario leading to enantiopure ribose is separation on a flat, but not necessarily chiral surface in the presence of a strong electric field capable of orienting highly polar derivatives of sugars. Portions of this work were presented to Mid-Atlantic Regional Meeting of ACS, Hershey, PA, USA, June 05, 2006.     

Use of a diploid cell line for detecting the toxic components in medical immunobiological preparations

Besides specific antigens medical immunobiological agents (MIBA) contain chemical compounds (formaldehyde, aluminium hydroxide and mercury salt, merthiolate) in permissible concentrations. Therefore, the investigation of MIBA and their components should involve methods studying the effect of chemical compounds on cells and their structural components. For this purpose WHO recommends to use cell cultures. The results obtained show that cell cultures (constant and diploid lines) allow the differentiation in the degree of toxicity of chemical compounds constituting MIBA. Merthiolate had the strongest irreversible lethal effect. The technique can prove useful for more accurate evaluation of toxicity in inactivated bacterial and viral vaccines as well as in serum preparations. Cell culture can be successfully used for the detection of toxic components in vaccines and serum drugs, with the final safety tested by their injection to animals.     

Bioinformatics meets user-centred design: a perspective

Designers have a saying that "the joy of an early release lasts but a short time. The bitterness of an unusable system lasts for years." It is indeed disappointing to discover that your data resources are not being used to their full potential. Not only have you invested your time, effort, and research grant on the project, but you may face costly redesigns if you want to improve the system later. This scenario would be less likely if the product was designed to provide users with exactly what they need, so that it is fit for purpose before its launch. We work at EMBL-European Bioinformatics Institute (EMBL-EBI), and we consult extensively with life science researchers to find out what they need from biological data resources. We have found that although users believe that the bioinformatics community is providing accurate and valuable data, they often find the interfaces to these resources tricky to use and navigate. We believe that if you can find out what your users want even before you create the first mock-up of a system, the final product will provide a better user experience. This would encourage more people to use the resource and they would have greater access to the data, which could ultimately lead to more scientific discoveries. In this paper, we explore the need for a user-centred design (UCD) strategy when designing bioinformatics resources and illustrate this with examples from our work at EMBL-EBI. Our aim is to introduce the reader to how selected UCD techniques may be successfully applied to software design for bioinformatics.     

Simultaneous Enantioseparation of Aldohexoses and Aldopentoses Derivatized With L‐Tryptophanamide by Reversed Phase HPLC Using Butylboronic Acid as a Complexation Reagent of Monosaccharides

Three aldohexoses, glucose, galactose, and mannose, and three aldopentoses, arabinose, xylose, and ribose, were derivatized with L‐tryptophanamide (L‐TrpNH₂) under alkaline conditions. Using a basic mobile phase (pH 9.2), the three aldohexoses or the three aldopentoses were simultaneously enantioseparated, respectively, but all the six monosaccharides could not be simultaneously enantioseparated. A large amount of nonreacted L‐TrpNH₂ was detected after the derivatized monosaccharides. In order to widen the separation window, a large portion of nonreacted L‐TrpNH₂ could be eliminated by liquid–liquid extraction with ethylacetate, and elution order of the derivatized monosaccharides and nonreacted L‐TrpNH₂ was found to be reversed using a neutral mobile phase. All of the six monosaccharides were simultaneously enantioseparated by reversed phase high‐performance liquid chromatography (HPLC) using InertSustainSwift C18 column (4.6 mm i.d. × 150 mm) and a mobile phase containing 180 mM phosphate buffer (pH 7.6), 1.5 mM butylboronic acid, and 5% acetonitrile at 40 °C. Nomenclature of D and L for monosaccharides is based on the configurations of the asymmetric C4 center for aldopentoses and C5 center for aldohexoses. It was found that the enantiomer elution order of these six monosaccharides and fucose in the proposed method conformed to be the absolute configuration of the C2 center. Chirality 27:417–421, 2015. © 2015 Wiley Periodicals, Inc.     

A new hypothesis for the origin of life

This hypothesis suggests that calcium chelating sugars, and especially ribose, have determined the nature of the first molecular systems. The self-organization capacities of these molecules enabled them to form regular arrays with certain salts. These arrays then evolved to form polysaccharides. In this first step, ribose and particularly -D-ribofuranose predominated over other prebiotic components. In a second step, the purines invaded these polysaccharides (3–5-polyribophosphodiester). The purines best suited for this were adenine and deoxyguanine, arising from the polymerization of HCN. Just as the polysaccharides reacted with purines, so the purines reacted with other small molecules and in particular, certain alkylating agents and water. After several methylation and oxidation reactions, adenine and deoxyguanine evolved to adenine, methylguanine, cytosine, uracil and thymine. Slow evolution of the prebiotic components gradually brought about a transition from a ribose world to an RNA world. The environment of this prebiotic RNA was different from that of modern RNA. For example, interaction of prebiotic RNA with water, calcium salts and certain zwitterionic molecules like the amino acids glycine and alanine was unavoidable. The interaction of these two small amino acids with calcium evolved to form transient anhydride bonds that quickly reverted to the initial state, or transformed to a peptide bond or to a more stable activated state, the oxazolone ring. The formation of this ring in double-stranded prebiotic RNA is the critical event that allowed the synthesis of new -L-amino acids. The positioning of the lateral sides of the amino acids inside the RNA suggests a stereochemical relationship that could explain the origin of the genetic code.     

Borate Minerals and Origin of the RNA World

The RNA World is generally thought to have been an important link between purely prebiotic (>3.7 Ga) chemistry and modern DNA/protein biochemistry. One concern about the RNA World hypothesis is the geochemical stability of ribose, the sugar moiety of RNA. Prebiotic stabilization of ribose by solutions associated with borate minerals, notably colemanite, ulexite, and kernite, has been proposed as one resolution to this difficulty. However, a critical unresolved issue is whether borate minerals existed in sufficient quantities on the primitive Earth, especially in the period when prebiotic synthesis processes leading to RNA took place. Although the oldest reported colemanite and ulexite are 330 Ma, and the oldest reported kernite, 19 Ma, boron isotope data and geologic context are consistent with an evaporitic borate precursor to 2400-2100 Ma borate deposits in the Liaoning and Jilin Provinces, China, as well as to tourmaline-group minerals at 3300–3450 Ma in the Barberton belt, South Africa. The oldest boron minerals for which the age of crystallization could be determined are the metamorphic tourmaline species schorl and dravite in the Isua complex (metamorphism between ca. 3650 and ca. 3600 Ma). Whether borates such as colemanite, ulexite and kernite were present in the Hadean (>4000 Ma) at the critical juncture when prebiotic molecules such as ribose required stabilization depends on whether a granitic continental crust had yet differentiated, because in its absence we see no means for boron to be sufficiently concentrated for borates to be precipitated.     

Two-stage fermentation process for the production of calcium magnesium acetate and propionate road deicers

Calcium magnesium acetate (CMA) and propionate (CMP) are environmentally benign deicing chemicals that can replace sodium chloride that is widely used on roads and highways at present for snow and ice control to provide safe driving conditions during winter. The price of CMA from petroleum-derived acetic acid is quite expensive. Anaerobic fermentations have not proven economical due to the low acid productivity and concentrations. A novel method for the production of CMA and CMP from lactose and whey permeate via a two-stage anoxic fermentation system, with calcium hydroxide for pH control is described in this paper. A homolactic bacterium Lactobacillus plantarum is used to convert lactose to calcium magnesium lactate (CML) in the first stage, and Propionicibacterium acidipropionici P200910 is used to convert CML to CMA and CMP in the second stage. In both stages, the conversion rates were 90% (w/w). Lactic acid productivity was 2.03 g/L/h in the first stage at a dilution ratio of 0.06 h⁻¹. Propionic and acetic acid yield was 1.79 g/L/h at a dilution rate of 0.05 h⁻¹. Calcium hydroxide addition did not significantly alter the overall yield of acids in either stage. However, the ratio of concentration of propionate to acetate in the final product changed from 3.0 when NaOH is used to 2.0 when lime is applied for pH control. After separation of the biomass, the liquid with a total concentration of 48–55 g/L of CMA and CMP can be processed to obtain a solid road deicer product.     

Influence of pH Modifiers and HPMC Viscosity Grades on Nicotine–Magnesium Aluminum Silicate Complex-Loaded Buccal Matrix Tablets

Hydroxypropyl methylcellulose (HPMC) tablets containing nicotine-magnesium aluminum silicate (NCT-MAS) complex particles and pH modifiers, namely, sodium chloride, citric acid, and magnesium hydroxide, were prepared using the direct compression method. The effects of HPMC viscosity grades and pH modifiers on NCT release and permeation of the matrix tablets were examined. The results showed that the higher the viscosity grade of HPMC that was used in the tablets, the lower was the unidirectional NCT release rate found. The unidirectional NCT permeation was not affected by the viscosity grade of HPMC because the NCT diffusion through the mucosal membrane was the rate-limiting step of the permeation. Incorporation of magnesium hydroxide could retard NCT release, whereas the enhancement of unidirectional NCT release was found in the tablets containing citric acid. Citric acid could inhibit NCT permeation due to the formation of protonated NCT in the swollen tablets at an acidic pH. Conversely, the NCT permeation rate increased with the use of magnesium hydroxide as a result of the neutral NCT that formed at a basic microenvironmental pH. The swollen HPMC tablets, with or without pH modifiers, gave sufficient adhesion to the mucosal membrane. Furthermore, the addition of magnesium hydroxide to the matrix tablets was the major factor in controlling buccal delivery of NCT. This study suggests that the NCT-MAS complex-loaded HPMC tablets, which contained magnesium hydroxide, are potential buccal delivery systems of NCT.     

Growth characteristics of a new methylomonad.

A methylomonad culture was isolated from pond water and examined as a potential source of single-cell protein. A medium containing magnesium sulfate, ammonium hydroxide, sodium phosphate, tap water, and methanol supported the growth of the isolate. Optimal growth conditions in batch cultures for the organism were: temperature, 30 to 33 degrees C; pH 7.1; and phosphate concentration, 0.015 M. The minimum doubling time obtained was 1.6 h. The specific growth rate in batch culture was dependent on the methanol concentration, reaching a maximum around 0.2% (wt/vol). Growth inhibition was apparent above 0.3% (wt/vol), and growth was completely inhibited above 4.6% (wt/vol) methanol. Although the inhibitory effect of formaldehyde on the specific growth rate was much greater than that of formate, the organism utilized formaldehyde, but not formate, as a sole carbon and energy source in batch cultures. The isolate was identified primarily by its inability to utilize any carbon source other than methanol and formaldehyde for growth. Although it is capable of rapid growth on methanol, the organism showed a very weak catalase activity. The amino acid content of the cells compared favorably with the reference levels for the essential amino acids specific by the Food and Agricultural Organization of the United Nations.