Mineral Surface Chemistry and Nanoparticle-aggregation Control Membrane Self-Assembly

The dynamics of prebiotic take-off: the transfer of functional RNA communities from mineral surfaces to vesicles

In this study, we propose a two-phase scenario for the origin of the first protocellular form of life, linking two RNA-world models by an explicit dynamical interface that simulates the transition of a metabolically cooperating RNA-replicator community from a mineral surface into a population of membrane vesicles. The two agent-based models: the Metabolically Coupled Replicator System (MCRS) and the Stochastic Corrector Model (SCM), are built on principles of systems chemistry, molecular biology, ecology and evolutionary biology. We show that the MCRS is easier to initiate from random RNA communities, while the SCM is more efficient at reducing the genetic assortment load during system growth and preadapted to later evolutionary transitions like chromosome formation, suggesting the former as a stepping stone to the later, protocellular stage. The switching between the two scenarios is shown to be dynamically feasible under a wide range of the parameter space of the merged model, allowing for the emergence of complex cooperative behaviours in metabolically coupled communities of RNA enzymes.

A Fusion-Growth Protocell Model Based on Vesicle Interactions with Pyrite Particles

Protocell models play a pivotal role in the exploration of the origin of life. Vesicles are one type of protocell model that have attracted much attention. Simple single-chain amphiphiles (SACs) and organic small molecules (OSMs) possess primitive relevance and were most likely the building blocks of protocells on the early Earth. OSM@SAC vesicles have been considered to be plausible protocell models. Pyrite (FeS2), a mineral with primitive relevance, is ubiquitous in nature and plays a crucial role in the exploration of the origin of life in the mineral-water interface scenario. "How do protocell models based on OSM@SAC vesicles interact with a mineral-water interface scenario that simulates a primitive Earth environment" remains an unresolved question. Hence, we select primitive relevant sodium monododecyl phosphate (SDP), isopentenol (IPN) and pyrite (FeS2) mineral particles to build a protocell model. The model investigates the basic physical and chemical properties of FeS2 particles and reveals the effects of the size, content and duration of interaction of FeS2 particles on IPN@SDP vesicles. This deepens the understanding of protocell growth mechanisms in scenarios of mineral-water interfaces in primitive Earth environments and provides new information for the exploration of the origin of life.

Dissolved metal ions and mineral-liposome hybrid systems: Underlying interactions, synthesis, and characterization

Liposomes are versatile lipid-based vesicles with interesting physicochemical properties, making them excellent candidates for interdisciplinary applications in the medicinal, biological, and environmental sciences. The synthesis of mineral-liposome hybrid systems lends normally inert vesicles with the catalytic, magnetic, electrical, and optical properties of the integrated mineral species. Such applications require an understanding of the physicochemical interactions between organic molecules and inorganic crystal structures. This review provides an overview on these interactions and details on synthesis and characterization methods for these systems.

Novel Chimeric Amino Acid-Fatty Alcohol Ester Amphiphiles Self-Assemble into Stable Primitive Membranes in Diverse Geological Settings

Primitive cells are believed to have been self-assembled vesicular structures with minimal metabolic components, that were capable of self-maintenance and self-propagation in early Earth geological settings. The coevolution and self-assembly of biomolecules, such as amphiphiles, peptides, and nucleic acids, or their precursors, were essential for protocell emergence. Here, we present a novel class of amphiphiles-amino acid-fatty alcohol esters-that self-assemble into stable primitive membrane compartments under a wide range of geochemical conditions. Glycine n-octyl ester (GOE) and isoleucine n-octyl ester (IOE), the condensation ester products of glycine or isoleucine with octanol (OcOH), are expected to form at a mild temperature by wet-dry cycles. The GOE forms micelles in acidic aqueous solutions (pH 2-7) and vesicles at intermediate pH (pH 7.3-8.2). When mixed with cosurfactants (octanoic acid [OcA]; OcOH, or decanol) in different mole fractions [X_Cosurfactant = 0.1-0.5], the vesicle stability range expands significantly to span the extremely acidic to mildly alkaline (pH 2-8) and extremely alkaline (pH 10-11) regions. Only a small mole fraction of cosurfactant [X_Cosurfactant = 0.1] is needed to make stable vesicular structures. Notably, these GOE-based vesicles are also stable in the presence of high concentrations of divalent cations, even at low pHs and in simulated Hadean seawater composition (without sulfate). To better understand the self-assembly behavior of GOE-based systems, we devised complementary molecular dynamics computer simulations for a series of mixed GOE/OcA systems under simulated acidic pHs. The resulting calculated critical packing parameter values and self-assembly behavior were consistent with our experimental findings. The IOE is expected to show similar self-assembly behavior. Thus, amino acid-fatty alcohol esters, a novel chimeric amphiphile class composed of an amino acid head group and a fatty alcohol tail, may have aided in building protocell membranes, which were stable in a wide variety of geochemical circumstances and were conducive to supporting replication and self-maintenance. The present work contributes to our body of work supporting our hypothesis for synergism and coevolution of (proto)biomolecules on early Earth.

Analysis of Ti- and Pb-based particles in the aqueous environment of Melbourne (Australia) via single particle ICP-MS

The analysis of natural and anthropogenic nanomaterials (NMs) in the environment is challenging and requires methods capable to identify and characterise structures on the nanoscale regarding particle number concentrations (PNCs), elemental composition, size, and mass distributions. In this study, we employed single particle inductively coupled plasma-mass spectrometry (SP ICP-MS) to investigate the occurrence of NMs in the Melbourne area (Australia) across 63 locations. Poisson statistics were used to discriminate between signals from nanoparticulate matter and ionic background. TiO2-based NMs were frequently detected and corresponding NM signals were calibated with an automated data processing platform. Additionally, a method utilising a larger mass bandpass was developed to screen for particulate high-mass elements. This procedure identified Pb-based NMs in various samples. The effects of different environmental matrices consisting of fresh, brackish, or seawater were mitigated with an aerosol dilution method reducing the introduction of salt into the plasma and avoiding signal drift. Signals from TiO2- and Pb-based NMs were counted, integrated, and subsequently calibrated to determine PNCs as well as mass and size distributions. PNCs, mean sizes, particulate masses, and ionic background levels were compared across different locations and environments.

Freshwater and Evaporite Brine Compositions on Hadean Earth: Priming the Origins of Life

The chemical composition of aqueous solutions during the Hadean era determined the availability of essential elements for prebiotic synthesis of the molecular building blocks of life. Here we conducted quantitative reaction path modeling of atmosphere-water-rock interactions over a range of environmental conditions to estimate freshwater and evaporite brine compositions. We then evaluated the solution chemistries for their potential to influence ribonucleotide synthesis and polymerization as well as protocell membrane stability. Specifically, solutions formed by komatiite and tonalite (primitive crustal rocks) weathering and evaporation-rehydration (drying-wetting) cycles were studied assuming neutral atmospheric composition over a wide range of values of atmospheric partial pressure of CO₂ (P_CO2) and temperatures (T). Solution pH decreased and total dissolved concentrations of inorganic P, Mg, Ca, Fe, and C (P_T, Mg_T, Ca_T, Fe_T, and C_T) increased with increasing P_CO2. The P_CO2 and T dictated how the solution evolved with regard to minerals precipitated and ions left in solution. At T = 75°C and P_CO2 < 0.05 atm, the concentration ratio of magnesium to calcium ion concentrations (Mg²⁺/Ca²⁺) was < 1 and predominantly metal aluminosilicates (including clays), dolomite, gibbsite, and pyrite (FeS₂) precipitated, whereas at P_CO2 > 0.05 atm, Mg²⁺/Ca²⁺ was > 1 and mainly magnesite, dolomite, pyrite, chalcedony (SiO₂), and kaolinite (Al₂Si₂O₅) precipitated. At T = 75°C and P_CO2 > 0.05 atm, hydroxyapatite (HAP) precipitated during weathering but not during evaporation, and so, P_T increased with each evaporation-rehydration cycle, while Mg_T, Ca_T, and Fe_T decreased as other minerals precipitated. At T = 75°C and P_CO2 ∼5 atm, reactions with komatiite provided end-of-weathering solutions with high enough Mg²⁺ concentrations to promote RNA-template directed and montmorillonite-promoted nonenzymatic RNA polymerization, but incompatible with protocell membranes; however, montmorillonite-promoted RNA polymerization could proceed with little or no Mg²⁺ present. Cyclically evaporating/rehydrating brines from komatiite weathering at T = 75°C and P_CO2 ∼5 atm yielded the following: (1) high P_T values that could promote ribonucleotide synthesis, and (2) low divalent cation concentrations compatible with amino acid-promoted, montmorillonite-catalyzed RNA polymerization and with protocell membranes, but too low for template-directed nonenzymatic RNA polymerization. For all P_CO2 values, Mg²⁺ and P_T concentrations decreased, whereas the HCO₃^- concentration increased within increasing temperature, due to the retrograde solubility of the minerals controlling these ions' concentrations; Fe²⁺ concentration increased because of prograde pyrite solubility. Tonalite weathering and cyclical wetting-drying reactions did not produce solution compositions favorable for promoting prebiotic RNA formation. Conversely, the ion concentrations compatible with protocell emergence, placed constraints on P_CO2 of early Earth's atmosphere. In summary: (1) prebiotic RNA synthesis and membrane self-assembly could have been achieved even under neutral atmosphere conditions by atmosphere-water-komatiite rock interactions; and (2) constraints on element availability for the origins of life and early P_CO2 were addressed by a single, globally operating mechanism of atmosphere-water-rock interactions without invoking special microenvironments. The present results support a facile origins-of-life hypothesis even under a neutral atmosphere as long as other favorable geophysical and planetary conditions are also met.

Protocells: Milestones and Recent Advances

The origin of life is still one of humankind's great mysteries. At the transition between nonliving and living matter, protocells, initially featureless aggregates of abiotic matter, gain the structure and functions necessary to fulfill the criteria of life. Research addressing protocells as a central element in this transition is diverse and increasingly interdisciplinary. The authors review current protocell concepts and research directions, address milestones, challenges and existing hypotheses in the context of conditions on the early Earth, and provide a concise overview of current protocell research methods.

Molecular Dynamics Simulation and Cryo-Electron Microscopy Investigation of AOT Surfactant Structure at the Hydrated Mica Surface

Structural properties of the anionic surfactant dioctyl sodium sulfosuccinate (AOT or Aerosol-OT) adsorbed on the mica surface were investigated by molecular dynamics simulation, including the effect of surface loading in the presence of monovalent and divalent cations. The simulations confirmed recent neutron reflectivity experiments that revealed the binding of anionic surfactant to the negatively charged surface via adsorbed cations. At low loading, cylindrical micelles formed on the surface, with sulfate head groups bound to the surface by water molecules or adsorbed cations. Cation bridging was observed in the presence of weakly hydrating monovalent cations, while sulfate groups interacted with strongly hydrating divalent cations through water bridges. The adsorbed micelle structure was confirmed experimentally with cryogenic electronic microscopy, which revealed micelles approximately 2 nm in diameter at the basal surface. At higher AOT loading, the simulations reveal adsorbed bilayers with similar surface binding mechanisms. Adsorbed micelles were slightly thicker (2.2–3.0 nm) than the corresponding bilayers (2.0–2.4 nm). Upon heating the low loading systems from 300 K to 350 K, the adsorbed micelles transformed to a more planar configuration resembling bilayers. The driving force for this transition is an increase in the number of sulfate head groups interacting directly with adsorbed cations.

Extraction and quantification of metal-containing nanoparticles in marine shellfish based on single particle inductively coupled plasma-mass spectrometry technique

Quantitative characterization of nanoparticles (NPs) in marine shellfish is critical to understanding the risks of bio-accumulation. Based on single particle (sp)ICP-MS and electron microscopy, a standardized protocol was developed to extract Ag, Au, and indigenous Ti-containing NPs from mussels. The optimal parameters are: dry sample extraction with tetramethylammonium hydroxide (TMAH), 5% (v/v) final concentration of TMAH, extraction at 25 ℃ for 12 h, and separation by centrifugation (3000 rpm for 5 min). The particle number recoveries of spiked Ag and Au NPs were 88 ± 0.9% and 95 ± 1.1%, respectively, while Ti-containing NPs had a particle number concentration of 8.2 × 10⁶ particles/mg and an average size of 70 nm in tested mussels. Furthermore, titanium oxide NPs, including rutile, anatase, and Magnéli phases (Ti_xO_2x-1) were found ubiquitously in 10 shellfish based on the optimal method. The particle number concentrations and average sizes of the Ti-containing NPs were 2.1 × 10⁶-8.4 × 10⁶ particles/mg and 70-80 nm, respectively. These Ti-containing NPs, such as TiO₂, accounted for about half of the Ti mass in shellfish, indicating that marine shellfish may be a significant sink for Ti-containing NPs.

Nanospeciation of metals and metalloids in volcanic ash using single particle inductively coupled plasma mass spectrometry

Volcanic activity is one of the main sources of natural nanoparticles. It has been found earlier that the concentration of toxic metals/metalloids in nanoparticles of volcanic ash may be one or two orders of magnitude higher than in bulk sample. However, fate and behavior of toxic metals/metalloids depend on the type of their binding to nanoparticles. Hence, element species adsorbed onto pyroclastic nanoparticles and individual nanophases of metal/metalloid oxides or salts should be distinguished. For the first time, the single particle inductively coupled plasma mass spectrometry has been applied to the nanospeciation of volcanic particles. Ashes of four volcanoes of Kamchatka (Russia) were under study. Nanoparticles were separated from bulk ash samples using coiled-tube field-flow fractionation. It has been shown that the nanospeciation of Ni, Zn, Ag, Cd, Tl, As, Pb, Bi, Te, and Hg is dependent on element and volcano. In most cases these elements can be found both as species absorbed onto pyroclastic nanoparticles and as individual nanophases. The ratios of individual nanophases and adsorbed species vary with the sample. In nanoparticles of Tolbachik volcano ash, Ni, Zn, Tl, and Hg are present only as individual nanophases, while Bi, As, Pb, Ag, Cd, and Te are found both as adsorbed species and individual nanophases. The results obtained open a new door into study on the chemical composition of volcanic ash nanoparticles and their fate in the environment.

Did Solid Surfaces Enable the Origin of Life?

In this perspective article, I discuss whether and how solid surfaces could have played a key role in the formation of membranous primitive cells on the early Earth. I argue why surface energy could have been used by prebiotic amphiphile assemblies for unique morphological transformations, and present recent experimental findings showing the surface-dependent formation and behavior of sophisticated lipid membrane structures. Finally, I discuss the possible unique contributions of such surface-adhered architectures to the transition from prebiotic matter to living systems.

Synthesis of lipid membranes for artificial cells

A major goal of synthetic biology is to understand the transition between non-living matter and life. The bottom-up development of an artificial cell would provide a minimal system with which to study the border between chemistry and biology. So far, a fully synthetic cell has remained elusive, but chemists are progressing towards this goal by reconstructing cellular subsystems. Cell boundaries, likely in the form of lipid membranes, were necessary for the emergence of life. In addition to providing a protective barrier between cellular cargo and the external environment, lipid compartments maintain homeostasis with other subsystems to regulate cellular processes. In this Review, we examine different chemical approaches to making cell-mimetic compartments. Synthetic strategies to drive membrane formation and function, including bioorthogonal ligations, dissipative self-assembly and reconstitution of biochemical pathways, are discussed. Chemical strategies aim to recreate the interactions between lipid membranes, the external environment and internal biomolecules, and will clarify our understanding of life at the interface of chemistry and biology.

Natural silicate nanoparticles: separation, characterization, and assessment of stability and perspectives of their use as reference nanomaterials

Natural nanomaterials, which play a very important role in environmental processes, are so far poorly studied. Firstly, the separation of nanoparticles from the bulk sample is a challenge. Secondly, the absence of reference natural nanomaterials makes it impossible to compare the results obtained by different researchers and develop a unified methodology for the separation and characterization of natural nanomaterials. Therefore, the development of reference natural nanomaterials is an urgent need of the environmental analytical chemistry. In this work, mineral nanoparticles (kaolinite, montmorillonite, muscovite, and quartz) have been studied as potential reference natural nanomaterials. A set of analytical methods including coiled-tube field-flow fractionation, scanning electron microscopy, dynamic light scattering, laser diffraction, inductively coupled plasma atomic emission, and mass spectrometry are applied to the separation and characterization of nanoparticles. It has been shown by laser diffraction that 93-98% of separated mineral nanoparticles are in the size range from about 40 to 300 nm, while 2-7% have size up to 830 nm. The size range of particles is confirmed by electron microscopy. Major (Al, Na, K, Ca, Fe), trace (Ti, Co, Cu, Zn, Tl, Pb, Bi, etc.), and rare earth elements have been determined in the suspensions of kaolinite, montmorillonite, and muscovite nanoparticles. Based on Al content, the concentration of mineral nanoparticles in suspensions is estimated. Agglomeration stability (consistency of size distribution) of nanoparticles at pH 6-8 is assessed. It has been shown that muscovite nanoparticles are stable at pH 7-8, whereas montmorillonite nanoparticles are stable only at pH 8 for at least 4 weeks. A noticeable agglomeration of kaolinite nanoparticles is observed at pH 6-8. Due to the low concentration of quartz nanoparticles, their characterization and stability assessment are hindered. The challenges of the development of reference natural nanomaterials are discussed.

Primitive Compartmentalization for the Sustainable Replication of Genetic Molecules

Sustainable replication and evolution of genetic molecules such as RNA are likely requisites for the emergence of life; however, these processes are easily affected by the appearance of parasitic molecules that replicate by relying on the function of other molecules, while not contributing to their replication. A possible mechanism to repress parasite amplification is compartmentalization that segregates parasitic molecules and limits their access to functional genetic molecules. Although extent cells encapsulate genomes within lipid-based membranes, more primitive materials or simple geological processes could have provided compartmentalization on early Earth. In this review, we summarize the current understanding of the types and roles of primitive compartmentalization regarding sustainable replication of genetic molecules, especially from the perspective of the prevention of parasite replication. In addition, we also describe the ability of several environments to selectively accumulate longer genetic molecules, which could also have helped select functional genetic molecules rather than fast-replicating short parasitic molecules.

Origin of Species before Origin of Life: The Role of Speciation in Chemical Evolution

Speciation, an evolutionary process by which new species form, is ultimately responsible for the incredible biodiversity that we observe on Earth every day. Such biodiversity is one of the critical features which contributes to the survivability of biospheres and modern life. While speciation and biodiversity have been amply studied in organismic evolution and modern life, it has not yet been applied to a great extent to understanding the evolutionary dynamics of primitive life. In particular, one unanswered question is at what point in the history of life did speciation as a phenomenon emerge in the first place. Here, we discuss the mechanisms by which speciation could have occurred before the origins of life in the context of chemical evolution. Specifically, we discuss that primitive compartments formed before the emergence of the last universal common ancestor (LUCA) could have provided a mechanism by which primitive chemical systems underwent speciation. In particular, we introduce a variety of primitive compartment structures, and associated functions, that may have plausibly been present on early Earth, followed by examples of both discriminate and indiscriminate speciation affected by primitive modes of compartmentalization. Finally, we discuss modern technologies, in particular, droplet microfluidics, that can be applied to studying speciation phenomena in the laboratory over short timescales. We hope that this discussion highlights the current areas of need in further studies on primitive speciation phenomena while simultaneously proposing directions as important areas of study to the origins of life.

The Role of Minerals in Events That Led to the Origin of Life

The role of minerals in the events that led to the origin of life is discussed with regard to (1) their catalytic role for the formation of RNA-like oligomers from their monomers and (2) their protective role for organic molecules formed in space that were delivered to planetary surfaces. Results obtained in the laboratory demonstrate that minerals do catalyze the oligomerization of ribonucleic acid (RNA) monomers to produce short RNA chains. Furthermore, and more importantly, these synthetic RNA chains formed by mineral catalysis serve as a template for the formation of complementary RNA chains, which is a significant finding that demonstrates the role of minerals in the origin of life. Simulation experiments run under Mars-like conditions have also shown that Mars analog minerals can shield the precursors of RNA and proteins against the harmful effects of UV and gamma radiation at the martian surface and 5 cm below the surface.

Nanoscale Anatomy of Iron-Silica Self-Organized Membranes: Implications for Prebiotic Chemistry

Iron-silica self-organized membranes, so-called chemical gardens, behave as fuel cells and catalyze the formation of amino/carboxylic acids and RNA nucleobases from organics that were available on early Earth. Despite their relevance for prebiotic chemistry, little is known about their structure and mineralogy at the nanoscale. Studied here are focused ion beam milled sections of iron-silica membranes, grown from synthetic and natural, alkaline, serpentinization-derived fluids thought to be widespread on early Earth. Electron microscopy shows they comprise amorphous silica and iron nanoparticles of large surface areas and inter/intraparticle porosities. Their construction resembles that of a heterogeneous catalyst, but they can also exhibit a bilayer structure. Surface-area measurements suggest that membranes grown from natural waters have even higher catalytic potential. Considering their geochemically plausible precipitation in the early hydrothermal systems where abiotic organics were produced, iron-silica membranes might have assisted the generation and organization of the first biologically relevant organics.

Development of Novel High-Resolution Size-Guided Turbidimetry-Enabled Particle Purification Liquid Chromatography (PPLC): Extracellular Vesicles and Membraneless Condensates in Focus

Acellular particles (extracellular vesicles and membraneless condensates) have important research, drug discovery, and therapeutic implications. However, their isolation and retrieval have faced enormous challenges, impeding their use. Here, a novel size-guided particle purification liquid chromatography (PPLC) is integrated into a turbidimetry-enabled system for dye-free isolation, online characterization, and retrieval of intact acellular particles from biofluids. The chromatographic separation of particles from different biofluids-semen, blood, urine, milk, and cell culture supernatants-is achieved using a first-in-class gradient size exclusion column (gSEC). Purified particles are collected using a fraction collector. Online UV-Vis monitoring reveals biofluid-dependent particle spectral differences, with semen being the most complex. Turbidimetry provides the accurate physical characterization of seminal particle (Sp) lipid contents, sizes, and concentrations, validated by a nanoparticle tracking analysis, transmission electron microscopy, and naphthopyrene assay. Furthermore, different fractions of purified Sps contain distinct DNA, RNA species, and protein compositions. The integration of Sp physical and compositional properties identifies two archetypal membrane-encased seminal extracellular vesicles (SEV)-notably SEV large (SEVL), SEV small (SEVS), and a novel nonarchetypalμμembraneless Sps, herein named membraneless condensates (MCs). This study demonstrates a comprehensive yet affordable platform for isolating, collecting, and analyzing acellular particles to facilitate extracellular particle research and applications in drug delivery and therapeutics. Ongoing efforts focus on increased resolution by tailoring bead/column chemistry for each biofluid type.

A Model Protometabolic Pathway Across Protocell Membranes Assisted by Photocatalytic Minerals

Protocell analogs (lipid vesicles) to modern cell membranes have been postulated as compartments that may have been involved in primordial metabolism during the transition from geochemistry to biochemistry on early Earth. The transduction of light energy into chemical energy for metabolism was a key step in the transition from the earliest metabolisms to phototrophy. Photocatalytic minerals may have served the role of enzymes during these transitional stages. Here, we demonstrate a simple photoheterotrophic protometabolism promoted by photocatalytic minerals across a model protocell (vesicle) membrane. These minerals in the extra-vesicular medium utilized light energy to drive a coupled, multi-step transmembrane electron transfer reaction (TMETR), while simultaneously generating a transmembrane pH gradient and reducing nicotinamide adenine dinucleotide (NAD+) to NADH within the vesicle. The proton gradient or chemiosmotic potential could have provided a basis for adenosine triphosphate (ATP) synthesis and NADH could potentially have driven further metabolic chemistry inside the protocells.

Natural, incidental, and engineered nanomaterials and their impacts on the Earth system

Nanomaterials are critical components in the Earth system’s past, present, and future characteristics and behavior. They have been present since Earth’s origin in great abundance. Life, from the earliest cells to modern humans, has evolved in intimate association with naturally occurring nanomaterials. This synergy began to shift considerably with human industrialization. Particularly since the Industrial Revolution some two-and-a-half centuries ago, incidental nanomaterials (produced unintentionally by human activity) have been continuously produced and distributed worldwide. In some areas, they now rival the amount of naturally occurring nanomaterials. In the past half-century, engineered nanomaterials have been produced in very small amounts relative to the other two types of nanomaterials, but still in large enough quantities to make them a consequential component of the planet. All nanomaterials, regardless of their origin, have distinct chemical and physical properties throughout their size range, clearly setting them apart from their macroscopic equivalents and necessitating careful study. Following major advances in experimental, computational, analytical, and field approaches, it is becoming possible to better assess and understand all types and origins of nanomaterials in the Earth system. It is also now possible to frame their immediate and long-term impact on environmental and human health at local, regional, and global scales.

Core-Shell Modeling of Light Scattering by Vesicles: Effect of Size, Contents, and Lamellarity

Having a fast, reliable method for characterizing vesicles is vital for their use as model cell membranes in biophysics, synthetic biology, and origins of life studies. Instead of the traditionally used Rayleigh-Gans-Debye approximation, we use an exact extended Lorenz-Mie solution for how core-shell particles scatter light to model vesicle turbidity. This approach enables accurate interpretations of simple turbidimetric measurements and is able to accurately model highly scattering vesicles, such as larger vesicles, those with multiple layers, and those with encapsulated material. We uncover several surprising features, including that vesicle lamellarity has a larger effect on sample turbidity than vesicle size and that the technique can be used to measure the membrane thickness of vesicles. We also examine potential misinterpretations of turbidimetry and discuss when measurements are limited by forward and multiple scattering and by the geometry of the instrument.

The Paleomineralogy of the Hadean Eon Revisited

A preliminary list of plausible near-surface minerals present during Earth’s Hadean Eon (>4.0 Ga) should be expanded to include: (1) phases that might have formed by precipitation of organic crystals prior to the rise of predation by cellular life; (2) minerals associated with large bolide impacts, especially through the generation of hydrothermal systems in circumferential fracture zones; and (3) local formation of minerals with relatively oxidized transition metals through abiological redox processes, such as photo-oxidation. Additional mineral diversity arises from the occurrence of some mineral species that form more than one ‘natural kind’, each with distinct chemical and morphological characteristics that arise by different paragenetic processes. Rare minerals, for example those containing essential B, Mo, or P, are not necessary for the origins of life. Rather, many common minerals incorporate those and other elements as trace and minor constituents. A rich variety of chemically reactive sites were thus available at the exposed surfaces of common Hadean rock-forming minerals.

Lipid vesicles chaperone an encapsulated RNA aptamer

The organization of molecules into cells is believed to have been critical for the emergence of living systems. Early protocells likely consisted of RNA functioning inside vesicles made of simple lipids. However, little is known about how encapsulation would affect the activity and folding of RNA. Here we find that confinement of the malachite green RNA aptamer inside fatty acid vesicles increases binding affinity and locally stabilizes the bound conformation of the RNA. The vesicle effectively ‘chaperones’ the aptamer, consistent with an excluded volume mechanism due to confinement. Protocellular organization thereby leads to a direct benefit for the RNA. Coupled with previously described mechanisms by which encapsulated RNA aids membrane growth, this effect illustrates how the membrane and RNA might cooperate for mutual benefit. Encapsulation could thus increase RNA fitness and the likelihood that functional sequences would emerge during the origin of life.

So far little is known about how encapsulation affects the activity and folding of RNA, which is of interest for understanding the origin of cellular life. Here the authors show that encapsulation of functional RNA in vesicles increases RNA activity and improves RNA folding through a biophysical confinement effect.

Mineral Surface-Templated Self-Assembling Systems: Case Studies from Nanoscience and Surface Science towards Origins of Life Research

An increasing body of evidence relates the wide range of benefits mineral surfaces offer for the development of early living systems, including adsorption of small molecules from the aqueous phase, formation of monomeric subunits and their subsequent polymerization, and supramolecular assembly of biopolymers and other biomolecules. Each of these processes was likely a necessary stage in the emergence of life on Earth. Here, we compile evidence that templating and enhancement of prebiotically-relevant self-assembling systems by mineral surfaces offers a route to increased structural, functional, and/or chemical complexity. This increase in complexity could have been achieved by early living systems before the advent of evolvable systems and would not have required the generally energetically unfavorable formation of covalent bonds such as phosphodiester or peptide bonds. In this review we will focus on various case studies of prebiotically-relevant mineral-templated self-assembling systems, including supramolecular assemblies of peptides and nucleic acids, from nanoscience and surface science. These fields contain valuable information that is not yet fully being utilized by the origins of life and astrobiology research communities. Some of the self-assemblies that we present can promote the formation of new mineral surfaces, similar to biomineralization, which can then catalyze more essential prebiotic reactions; this could have resulted in a symbiotic feedback loop by which geology and primitive pre-living systems were closely linked to one another even before life’s origin. We hope that the ideas presented herein will seed some interesting discussions and new collaborations between nanoscience/surface science researchers and origins of life/astrobiology researchers.

Modified Lipid Extraction Methods for Deep Subsurface Shale

Growing interest in the utilization of black shales for hydrocarbon development and environmental applications has spurred investigations of microbial functional diversity in the deep subsurface shale ecosystem. Lipid biomarker analyses including phospholipid fatty acids (PLFAs) and diglyceride fatty acids (DGFAs) represent sensitive tools for estimating biomass and characterizing the diversity of microbial communities. However, complex shale matrix properties create immense challenges for microbial lipid extraction procedures. Here, we test three different lipid extraction methods: modified Bligh and Dyer (mBD), Folch (FOL), and microwave assisted extraction (MAE), to examine their ability in the recovery and reproducibility of lipid biomarkers in deeply buried shales. The lipid biomarkers were analyzed as fatty acid methyl esters (FAMEs) with the GC-MS, and the average PL-FAME yield ranged from 67 to 400 pmol/g, while the average DG-FAME yield ranged from 600 to 3,000 pmol/g. The biomarker yields in the intact phospholipid Bligh and Dyer treatment (mBD + Phos + POPC), the Folch, the Bligh and Dyer citrate buffer (mBD-Cit), and the MAE treatments were all relatively higher and statistically similar compared to the other extraction treatments for both PLFAs and DGFAs. The biomarker yields were however highly variable within replicates for most extraction treatments, although the mBD + Phos + POPC treatment had relatively better reproducibility in the consistent fatty acid profiles. This variability across treatments which is associated with the highly complex nature of deeply buried shale matrix, further necessitates customized methodological developments for the improvement of lipid biomarker recovery.