A possible role of fluctuating clay-water systems in the production of ordered prebiotic oligomers

Summary A model is proposed for the intermediate stages of prebiotic evolution, based on the characteristics of the adsorption and condensation of amino acids and nucleotides on the surface area of clay minerals in a fluctuating environment. Template replication and translation of adsorbed oligonucleotides and catalytic effects by peptide products on further condensation are proposed, due to specific properties of hypohydrous clay surfaces as well as the biomolecules themselves. Experimental evidence supports some of the proposed interactions, and all of them can be tested experimentally.on leave from the Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel, 1975–76     

土壤矿物与微生物相互作用的机理及其环境效应

土壤矿物与微生物相互作用是地球表层系统中重要的生态过程.微生物或生物分子与矿物间的吸附(粘附)是两者相互作用的基础.吸附(粘附)是一个由分子间力、静电力、疏水作用力、氢键和空间位阻效应等多种作用力或作用因素共同决定、影响的物理化学过程.因此,微生物和矿物的表面性质如表面电荷、疏水性和它们所处的环境条件如pH、电解质浓度、温度等,都影响着矿物-微生物吸附(粘附)过程.微生物细胞或酶可吸附于矿物表面,其结果是细胞代谢或酶活性会发生明显变化,并进一步影响土壤中诸多相关的生态、环境过程.结合4种典型的初始吸附理论:表面自由能热力学理论、DLVO理论、吸附等温线理论和表面复合物理论及本课题组近年来的研究成果,对土壤矿物与微生物相互作用的类型、机理、作用力和现代研究技术等方面的最新研究进展进行了较为全面的论述,对土壤矿物-微生物相互作用的环境效应进行了讨论,并就该领域今后研究工作的特点及应关注的问题进行了展望.     

The possible role of solid surface area in condensation reactions during chemical evolution: Reevaluation

Summary Published data on adsorption and condensation of amino acids, purine and pyrimidine bases, sugars, nucleosides, and nucleotides are analyzed in connection with Bernal's hypothesis that clays and other minerals may have provided the most likely surface for adsorption and condensation of these molecules in prebiotic times. Using surface concentration and reaction rate as the main criteria for the feasibility of condensation reactions, four types of prebiotic environments were analyzed: (1) an ocean-sediment system, (2) a dehydrated lagoon bed produced by evaporation, (3) the surface of a frozen sediment, and (4) a fluctuating system where hydration (rainstorms, tidal variations, flooding) and dehydration (evaporation) take place in a cyclic manner. With the possible exception of nucleotides, low adsorption of organomonomers on sediment surfaces of a prebiotic ocean (pH 8) is expected, and significant condensation is considered unlikely. In dehydrated and frozen systems, high surface concentrations are probable and condensation is more likely. In fluctuating environments, condensation rates will be enhanced and the size distribution of the oligomers formed during dehydration may be influenced by a redistribution mechanism in which adsorbed oligomers and monomers are desorbed and redistributed on the solid surface during the next hydration-dehydration cycle.On leave from the Faculty of Agriculture, Rehovot, The Hebrew University of Jerusalem, Israel.     

Modulation of biomolecular phase behavior by metal ions

Liquid–liquid phase separation (LLPS) appears to be a newly appreciated aspect of the cellular organization of biomolecules that leads to the formation of membraneless organelles (MLOs). MLOs generate distinct microenvironments where particular biomolecules are highly concentrated compared to those in the surrounding environment. Their thermodynamically driven formation is reversible, and their liquid nature allows them to fuse with each other. Dysfunctional biomolecular condensation is associated with human diseases. Pathological states of MLOs may originate from the mutation of proteins or may be induced by other factors. In most aberrant MLOs, transient interactions are replaced by stronger and more rigid interactions, preventing their dissolution, and causing their uncontrolled growth and dysfunction. For these reasons, there is great interest in identifying factors that modulate LLPS. In this review, we discuss an enigmatic and mostly unexplored aspect of this process, namely, the regulatory effects of metal ions on the phase behavior of biomolecules.     

Resolution of sertraline with (R)-mandelic acid: chiral discrimination mechanism study

The chiral discrimination mechanism in the resolution of sertraline with mandelic acid was investigated by examining the weak intermolecular interactions (such as hydrogen bond, CH/π, and van der Waals interactions) and molecular packing difference in crystal structures of the resulting diastereomeric salts. A new one-dimensional chain-like hydrogen-bonding network and unique supramolecular packing mode are disclosed. The investigation demonstrated that stable hydrogen-bonding pattern, herringbone-like arrangement of aromatic rings, and planar boundary surface in the hydrophobic region are the three most important structural characteristics expected in less soluble diastereomeric salts. The existence and magnitude of hydrogen bond, CH/π interaction, and van der Waals interaction related to three characteristic structures, determine the stability of diastereomeric salt. The hydrogen bond is not necessarily the dominant factor while the synergy and optimization of all weak intermolecular interactions attribute to the chiral recognition.     

Salinity Effects on the Adsorption of Nucleic Acid Compounds on Na-Montmorillonite: a Prebiotic Chemistry Experiment

Any proposed model of Earth’s primitive environments requires a combination of geochemical variables. Many experiments are prepared in aqueous solutions and in the presence of minerals. However, most sorption experiments are performed in distilled water, and just a few in seawater analogues, mostly inconsistent with a representative primitive ocean model. Therefore, it is necessary to perform experiments that consider the composition and concentration of dissolved salts in the early ocean to understand how these variables could have affected the absorption of organic molecules into minerals. In this work, the adsorption of adenine, adenosine, and 5’AMP onto Na⁺montmorillonite was studied using a primitive ocean analog (4.0 Ga) from experimental and computational approaches. The order of sorption of the molecules was: 5’AMP?>?adenine > adenosine. Infrared spectra showed that the interaction between these molecules and montmorillonite occurs through the NH₂ group. In addition, electrostatic interaction between negatively charged montmorillonite and positively charge N1 of these molecules could occur. Results indicate that dissolved salts affect the sorption in all cases; the size and structure of each organic molecule influence the amount sorbed. Specifically, the X-ray diffraction patterns show that dissolved salts occupy the interlayer space in Na-montmorillonite and compete with organic molecules for available sites. The adsorption capacity is clearly affected by dissolved salts in thermodynamic terms as deduced by isotherm models. Indeed, molecular dynamic models suggest that salts are absorbed in the interlamellar space and can interact with oxygen atoms exposed in the edges of clay or in its surface, reducing the sorption of the organic molecules. This research shows that the sorption process could be affected by high concentration of salts, since ions and organic molecules may compete for available sites on inorganic surfaces. Salt concentration in primitive oceans may have strongly affected the sorption, and hence the concentration processes of organic molecules on minerals.     

Isothermal Titration Calorimetry of Chiral Polymeric Nanoparticles

Chiral polymeric nanoparticles are of prime importance, mainly due to their enantioselective potential, for many applications such as catalysis and chiral separation in chromatography. In this article we report on the preparation of chiral polymeric nanoparticles by miniemulsion polymerization. In addition, we describe the use of isothermal titration calorimetry (ITC) to measure the chiral interactions and the energetics of the adsorption of enantiomers from aqueous solutions onto chiral polymeric nanoparticles. The characterization of chirality in nano‐systems is a very challenging task; here, we demonstrate that ITC can be used to accurately determine the thermodynamic parameters associated with the chiral interactions of nanoparticles. The use of ITC to measure the energetics of chiral interactions and recognition at the surfaces of chiral nanoparticles can be applied to other nanoscale chiral systems and can provide further insight into the chiral discrimination processes of nanomaterials. Chirality 27:613–618, 2015. © 2015 Wiley Periodicals, Inc.     

Resolution of 2-chloromandelic acid with (R)-(+)-N-benzyl-1-phenylethylamine: chiral discrimination mechanism

During the resolution of 2-chloromandelic acid with (R)-(+)-N-benzyl-1-phenylethylamine, the crystals of the less soluble salt were grown, and their structure were determined and presented. The chiral discrimination mechanism was investigated by examining the weak intermolecular interactions (such as hydrogen bond, CH/π, and van der Waals interactions) and molecular packing mode in crystal structure of the less soluble diastereomeric salt. A one-dimensional double-chain hydrogen-bonding network and a "lock-and-key" supramolecular packing mode are disclosed. The investigation demonstrates that hydrophobic layers with corrugated surfaces can fit into the grooves of one another to realize a compact packing, when the molecular structure of resolving agent is much larger than that of the racemate. This "lock-and-key" assembly is recognized to be another characteristic of molecular packing contributing to the chiral discrimination, in addition to the well-known sandwich-like packing by hydrophobic layers with planar boundary surfaces.     

Development of Iron-Phosphate Biofilms on Pyritic Mine Waste Rock Surfaces Previously Treated with Natural Phosphate Rocks

Various treatments have been proposed to attenuate and eventually inhibit the generation of acid mine drainage (AMD) or acid-rock drainage (ARD). The addition of Natural Phosphate Rocks (NPR) to mining wastes has been shown to reduce acid generation. The biogeochemical reactions underlying the phosphate precipitation reactions are however poorly understood, even though the chemical reactions are well defined. The present study was designed to study the role of solution chemistry and bacterial activity on phosphate precipitation on waste rock surfaces. Waste rock samples (rich in sulphides) previously weathered for 989 days in the presence of NPR were submersed in 2 different phosphate-rich growth media in order to enhance the growth of acidophilic and neutrophilic bacteria. DAPI and FISH analyses revealed that most cells belonged to the bacteria domain, and that alpha- and beta-proteobacteria were the dominant neutrophiles. ESEM, SEM and TEM observations of the samples revealed the presence of a biofilm on the surface of the rocks at both pH conditions. Bacteria and fine-grained precipitates were trapped in an exopolymer matrix. At low pH, the formation of fine precipitates rich in Fe and P within the biofilm corresponded to a decline of phosphate concentrations in the growth medium. This was in agreement with the solubility calculations which indicated that the medium became over-saturated with respect to some Fe-phosphate minerals. In the pH neutral system, solubility calculations indicated that Ca- and Mg-phosphate minerals were stable, but they were not detected in the biofilm. Solubility calculations also indicated that vivianite became unstable over time, which could explain the release of soluble phosphate over time in the pH neutral system. Our results showed that precipitation reactions played an important role in the solubility of phosphate in both systems, but a series of complex nucleation reactions involving bacterial exopolymers and the presence of microenvironments within the biofilms were likely important factors as well. Our findings also imply that the reduction of acid generation in NPR-treated waste rocks could be due in part to the formation of biofilms on the rock surfaces because the biofilms would act as a physical and chemcial barrier to limit the extent of pyrite oxidation.     

Abiotic factors affecting the toxicity of lead to fungi.

The toxicity of lead (Pb) to fungi in pure culture was influenced by several abiotic factors: pH, inorganic anions, clay minerals, and particulate (humic acid) and soluble organic matter. The toxicity of Pb was potentiated under acidic conditions (pH 5 and 6), and phosphate or carbonate anions reduced the toxicity, apparently as a result of the formation of sparingly soluble Pb salts. Clay minerals (montmorillonite greater than attapulgite greater than kaolinite) and particulate humic acid protected against the toxicity of Pb, presumably as the result of sorption, by cation exchange of the Pb to the exchange complexes, which reduced its availability for uptake by the fungi. Soluble organics, such as tryptone, yeast extract, cysteine, succinic acid, and increasing concentrations of neopeptone, also reduced the toxicity of Pb.     

Abiotic factors affecting the toxicity of lead to fungi.

The toxicity of lead (Pb) to fungi in pure culture was influenced by several abiotic factors: pH, inorganic anions, clay minerals, and particulate (humic acid) and soluble organic matter. The toxicity of Pb was potentiated under acidic conditions (pH 5 and 6), and phosphate or carbonate anions reduced the toxicity, apparently as a result of the formation of sparingly soluble Pb salts. Clay minerals (montmorillonite greater than attapulgite greater than kaolinite) and particulate humic acid protected against the toxicity of Pb, presumably as the result of sorption, by cation exchange of the Pb to the exchange complexes, which reduced its availability for uptake by the fungi. Soluble organics, such as tryptone, yeast extract, cysteine, succinic acid, and increasing concentrations of neopeptone, also reduced the toxicity of Pb.     

Reactions of boron with soils

Boron is an essential micronutrient for plants, but the range between deficient and toxic B concentration is smaller than for any other nutrient element. Plants respond directly to the activity of B in soil solution and only indirectly to B adsorbed on soil constituents. Soil factors affecting availability of B to plants are: pH, texture, moisture, temperature, organic matter and clay mineralogy. Boron adsorbing surfaces in soils are: aluminium and iron oxides, magnesium hydroxide, clay minerals, calcium carbonate, and organic matter. Boron adsorption reactions can be described empirically using the Langmuir adsorption isotherm equation, the Freundlich adsorption isotherm equation, and the phenomenological Keren model. Chemical models such as the constant capacitance model, the triple layer model, and the Stern VSC-VSP model can describe B adsorption over changing conditions of solution pH and B concentration. Boron desorption reactions often exhibit hysteresis. The rate of B desorption can be described using the first order rate equation, the Elovich reaction rate equation, and the power function equation.     

The development of high-throughput screening approaches for stem cell engineering

It has become increasingly clear that both soluble factors, such as growth factors, and insoluble factors, including the surfaces on which cells grow, can have controlling effects on stem cell behavior and differentiation. While much progress has been made in biomaterial design and application, the rational design of biomaterial cues to direct stem cell behavior and differentiation remains challenging. Recent advances in automated, high-throughput methods for synthesizing and screening combinatorial biomaterial libraries and cellular microenvironments promise to accelerate the discovery of factors that control stem cell behavior. Specific examples include miniaturized, automated, combinatorial material synthesis and extracellular matrix screening methods as well microarrayed methods for creating local microenvironments of soluble factors, such as small molecules, siRNA, and other signaling molecules.     

Catalytic effects of Murchison Material: Prebiotic Synthesis and Degradation of RNA Precursors

Mineral components of the Murchison meteorite were investigated in terms of potential catalytic effects on synthetic and hydrolytic reactions related to ribonucleic acid. We found that the mineral surfaces catalyzed condensation reactions of formamide to form carboxylic acids, amino acids, nucleobases and sugar precursors. These results suggest that formamide condensation reactions in the parent bodies of carbonaceous meteorites could give rise to multiple organic compounds thought to be required for the emergence of life. Previous studies have demonstrated similar catalytic effects for mineral assemblies likely to have been present in the early Earth environment. The minerals had little or no effect in promoting hydrolysis of RNA (24mer of polyadenylic acid) at 80°C over a pH range from 4.2 to 9.3. RNA was most stable in the neutral pH range, with a half-life ~5 h, but at higher and lower pH ranges the half-life decreased to ~1 h. These results suggest that if RNA was somehow incorporated into a primitive form of RNA-based thermophilic life, either it must be protected from random hydrolytic events, or the rate of synthesis must exceed the rate of hydrolysis.     

Nucleic Acids Bind to Nanoparticulate iron (II) Monosulphide in Aqueous Solutions

In the hydrothermal FeS-world origin of life scenarios nucleic acids are suggested to bind to iron (II) monosulphide precipitated from the reaction between hydrothermal sulphidic vent solutions and iron-bearing oceanic water. In lower temperature systems, the first precipitate from this process is nanoparticulate, metastable FeSm with a mackinawite structure. Although the interactions between bulk crystalline iron sulphide minerals and nucleic acids have been reported, their reaction with nanoparticulate FeSm has not previously been investigated. We investigated the binding of different nucleic acids, and their constituents, to freshly precipitated, nanoparticulate FeSm. The degree to which the organic molecules interacted with FeSm is chromosomal DNA > RNA > oligomeric DNA > deoxadenosine monophosphate approximately deoxyadenosine approximately adenine. Although we found that FeSm does not fluoresce within the visible spectrum and there is no quantum confinement effect seen in the absorption, the mechanism of linkage of the FeSm to these biomolecules appears to be primarily electrostatic and similar to that found for the attachment of ZnS quantum dots. The results of a preliminary study of similar reactions with nanoparticulate CuS further supported the suggestion that the interaction mechanism was generic for nanoparticulate transition metal sulphides. In terms of the FeS-world hypothesis, the results of this study further support the idea that sulphide minerals precipitated at hydrothermal vents interact with biomolecules and could have assisted in the formation and polymerisation of nucleic acids.     

Mineral Surface Directed Membrane Assembly

The transition from non-living to living matter may have resulted from the self-organizing properties of organic molecules and their interactions with a chemically rich inorganic environment. We have shown that a solution containing RNA, fatty acids and clay produces structures that contain a potentially catalytic surface (clay) and a potential informational biopolymer (RNA) encapsulated within a membrane. This highlights the ability of mineral surfaces to bring together and organize key components of primordial life. We have extended our analysis of mineral-mediated vesicle catalysis to include other natural minerals and synthetic surfaces of varying shape, size, and charge density. Our results show that while RNA polymerization on minerals may be restricted to the surface environment provided by montmorillonite, vesicle formation is enhanced in the presence of disparate types of surfaces. A model is presented in which new sheets of amphiphiles form just proximal to a surface. Similar interactions between amphiphiles and minerals on early Earth may have resulted in the encapsulation of a diverse array of mineral particulates with catalytic properties.     

Toward an understanding of biochemical equilibria within living cells

Four types of environmental effects that can affect macromolecular reactions in a living cell are defined: nonspecific intermolecular interactions, side reactions, partitioning between microenvironments, and surface interactions. Methods for investigating these interactions and their influence on target reactions in vitro are reviewed. Methods employed to characterize conformational and association equilibria in vivo are reviewed and difficulties in their interpretation cataloged. It is concluded that, in order to be amenable to unambiguous interpretation, in vivo studies must be complemented by in vitro studies carried out in well-characterized and controllable media designed to contain key elements of selected intracellular microenvironments.     

Terrestrial and extraterrestrial sources of molecular homochirality

The unique chirality of biomolecules is reviewed, and the prebiotic requirement for the absolute chiral homogeneity of such molecules prior to their capability of self-replication is emphasized. Biotic and abiotic theories embracing both chance and determinate mechanisms which have been proposed for the origin of terrestrial chiral molecules are briefly summarized and evaluated, as are abiotic mechanisms for the subsequent amplification of the small enantiomeric excesses (e.e.s) in the chiral molecules which might be formed by such processes. While amplification mechanisms are readily validated experimentally and are potentially viable on the primitive Earth, it is concluded that all terrestrial mechanisms proposed for the origin of chirality have one or more limitations which make them either intrinsically invalid or highly improbable in the chaotic and turbulent environment of the prebiotic Earth. To circumvent these difficulties we have proposed an extraterrestrial scenario for the production of terrestrial chirality in which circularly polarized synchrotron radiation from the neutron star remnant of a supernova interacts with the organic mantles on interstellar grains, producing chiral molecules by the partial asymmetric photolysis of racemic constituent in the mantles, after which the interstellar grains with their enantiomerically enriched mantles are transported to Earth either by direct accretion or through cometary impact. At this point one of the known terrestrial e.e. enrichment mechanisms could promote the small extraterrestrially produced e.e.s. into the state of chiral homogeneity required for self-replicating biomolecules.     

Model isolations of nucleic acids from prokaryotic and eukaryotic sources using an organic/aqueous biphasic system

Nucleic acids were extracted from bacteria and yeast, using a biphasic system created by mixing a water-miscible, organic solvent with an aqueous salt solution. Nucleic acids were separated from the majority of host-contaminating proteins without using chaotrophic agents such as guanidine salts, phenol or chloroform, which are known to be hazardous. Isolated DNA is sufficiently pure for use in the polymerase chain reaction (PCR).     

Protein expression profiling during chick retinal maturation: a proteomics-based approach

Background

We describe a biosensor platform for monitoring molecular interactions that is based on the combination of a defined nano-porous silicon surface, coupled to light interferometry. This platform allows the label-free detection of protein-protein and protein-DNA interactions in defined, as well as complex protein mixtures. The silicon surface can be functionalized to be compatible with traditional carboxyl immobilization chemistries, as well as with aldehyde-hydrazine bioconjugation chemistries.

Results

We demonstrate the utility of the new platform in measuring protein-protein interactions of purified products in buffer, in complex mixtures, and in the presence of different organic solvent spikes, such as DMSO and DMF, as these are commonly used in screening chemical compound libraries.

Conclusion

Nano-porous silicon, when combined with white light interferometry, is a powerful technique for the measurement of protein-protein interactions. In addition to studying the binary interactions of biomolecules in clean buffer systems, the newly developed surfaces are also suited for studying interactions in complex samples, such as plasma.