The possible origin of the first cell biosystem in the thermal subsurface environment of the earth.

Bacteria are the simplest living biosystems or organisms that exhibit all the characteristics of life. As such, they are excellent models to examine the cell as the basic unit of life and the cell theory which states that all organisms are composed of one or more similar cells. In this article I examine the hypothesis that the primordial soup so often referred to in science was possibly an oil/water interface and/or emulsion in the Earth's, warm, anaerobic subsurface. This warm subsurface location, protected from surface radiation, could have been a favourable location for the assembly of the first bacterial cells on the Earth capable of growth and controlled division or the first biosystem.     

Self-assembly of the first cells in a hydrophobic environment with hydrogen as the energy source.

Two fundamental questions in biology are how and where the first cell(s) self-assembled under anoxic conditions on the Earth. The possibility is explored that life first self-assembled in a hydrophobic environment in the subsurface protected from radiation with ubiquitous hydrogen as the likely universal energy source.     

Living nanovesicles--chemical and physical survival strategies of primordial biosystems

Life on Earth and Mars could have started with self-assembled nanovesicles similar to the present nanobacteria (NB). To resist extreme environmental stress situations and periods of nutritional deprivation, nanovesicles would have had a chemical composition protected by a closed mineralized compartment, facilitating their development in a primordial soup, or other early wet environment. Their survivability would have been enhanced if they had mechanisms for metabolic communication, and an ability to collect primordially available energy forms. Here, we establish an irreducible model system for life formation starting with NB.     

Modelling the Interior Structure of Enceladus Based on the 2014’s Cassini Gravity Data

We present a model for the internal structure of Saturn’s moon Enceladus. This model allows us to estimate the physical conditions at the bottom of the satellite’s potential subsurface water reservoir and to determine the radial distribution of pressure and gravity. This leads to a better understanding of the physical and chemical conditions at the water/rock boundary. This boundary is the most promising area on icy moons for astrobiological studies as it could serve as a potential habitat for extraterrestrial life similar to terrestrial microbes that inhabit rocky mounds on Earth’s sea floors.     

Hypothesis: the origin of life in a hydrogel environment

A hypothesis is proposed that the first cell(s) on the Earth assembled in a hydrogel environment. Gel environments are capable of retaining water, oily hydrocarbons, solutes, and gas bubbles, and are capable of carrying out many functions, even in the absence of a membrane. Thus, the gel-like environment may have conferred distinct advantages for the assembly of the first cell(s).     

A theory for the origin of a self-replicating chemical system. I: Natural selection of the autogen from short,random oligomers

Summary A theory is described for the origin of a simple chemical system named an autogen, consisting of two short oligonucleotide sequences coding for two simple catalytic peptides. If the theory is valid, under appropriate conditions the autogen would be capable of self-reproduction in a truly genetic process involving both replication and translation. Limited catalytic ability, short oligomer sequences, and low selectivities leading to sloppy information transfer processes are shown to be adequate for the origin of the autogen from random background oligomers. A series of discrete steps, each highly probable if certain minimum requirements and boundary conditions are satisfied, lead to exponential increase in population of all components in the system due to autocatalysis and hypercyclic organization. Nucleation of the components and exponential increase to macroscopic amounts could occur in times on the order of weeks. The feasibility of the theory depends on a number of factors, including the capability of simple protoenzymes to provide moderate enhancements of the accuracies of replication and translation and the likelihood of finding an environment where all of the required processes can occur simultaneously. Regardless of whether or not the specific form proposed for the autogen proves to be feasible, the theory suggests that the first self-replicating chemical systems may have been extremely simple, and that the period of time required for chemical evolution prior to Darwinian natural selection may have been far shorter than generally assumed. Due to the short time required, this theory, unlike others on the origin of genetic processes, is potentially capable of direct experimental verification. A number of prerequisites leading up to such an experiment are suggested, and some have been fulfilled. If successful, such an experiment would be the first laboratory demonstration of the spontaneous emergence by natural selection of a genetic, self-replicating, and evolving molecular system, and might represent the first step in the prebiotic environment of true Darwinian evolution toward a living cell.     

Prebiotic phosphate: a problem insoluble in water ? ]

It is well-known that in water phosphate readily reacts with calcium, precipitating as insoluble apatite. How phosphorus could have been available for prebiotic reactions is still an open problem. We suggest that phosphorus-containing compounds might have accumulated in a hydrophobic medium, since the absence of calcium ions would have prevented them from precipitating as apatite. Hydrophobic compounds may have been synthesized on the early Earth through the polymerization of methane or through Fischer-Tropsch-type reactions. Moreover, hydrophobic compounds would have been delivered to the early Earth by extraterrestrial infall. In previous articles (Morchio and Traverso [1999], Morchio et al. [2001]) we suggested that such hydrophobic material would have formed a hydrophobic layer on the surface of the sea, which would have provided an environment thermodynamically more suitable than water for the concentration and polymerization of organic molecules fundamental to life, particularly amino acids and (pyrimidine) bases. It may be hypothesized that elemental phosphorus or phosphorus-containing compounds (such as phosphite) deriving from volcanic eruptions would have ended up raining down into the hydrophobic layer, accumulating due to the absence of calcium ions, in an environment protected against hydrolysis. Phosphorus-containing compounds might have interacted with hydrophobic molecules in the layer giving rise to polymers. In particular, phosphite might have reacted with the hydrophobic amino acids, giving rise to phosphoamino acids, which, in turn, might have interacted with pyrimidine bases (relatively abundant in the layer) giving rise to peptides and oligonucleotide-like polymers. Indeed, it has been experimentally shown (Zhou et al. [1996]) that, in an anhydrous organic medium (pyridine), dialkilphosphite reacts with amino acids to form phosphoamino acids, which interact with pyrimidine nucleosides to give nucleotides, short oligonucleotides and phosphoryl peptides.     

Microbial diversity of deep-sea extremophiles--Piezophiles, Hyperthermophiles, and subsurface microorganisms]

Knowledge of our Planet's biosphere has increased tremendously during the last 10 to 20 years. In the field of Microbiology in particular, scientists have discovered novel "extremophiles", microorganisms capable of living in extreme environments such as highly acidic or alkaline conditions, at high salt concentration, with no oxygen, extreme temperatures (as low as -20 degrees C and as high as 300 degrees C), at high concentrations of heavy metals and in high pressure environments such as the deep-sea. It is apparent that microorganisms can exist in any extreme environment of the Earth, yet already scientists have started to look for life on other planets; the so-called "Exobiology" project. But as yet we have little knowledge of the deep-sea and subsurface biosphere of our own planet. We believe that we should elucidate the Biodiversity of Earth more thoroughly before exploring life on other planets, and these attempts would provide deeper insight into clarifying the existence of extraterrestrial life. We focused on two deep-sea extremophiles in this article; one is "Piezophiles", and another is "Hyperthermophiles". Piezophiles are typical microorganisms adapted to high-pressure and cold temperature environments, and located in deep-sea bottom. Otherwise, hyperthermophiles are living in high temperature environment, and located at around the hydrothermal vent systems in deep-sea. They are not typical deep-sea microorganisms, but they can grow well at high-pressure condition, just like piezophiles. Deming and Baross mentioned that most of the hyperthermophilic archaea isolated from deep-sea hydrothermal vents are able to grow under conditions of high temperature and pressure, and in most cases their optimal pressure for growth was greater than the environmental pressure they were isolated from. It is possible that originally their native environment may have been deeper than the sea floor and that there had to be a deeper biosphere. This implication suggests that the deep-sea hydrothermal vents are the windows to a deep subsurface biosphere. A vast array of chemoautotrophic deep-sea animal communities have been found to exist in cold seep environments, and most of these animals are common with those found in hydrothermal vent environments. Thus, it is possible to consider that the cold seeps are also one of slit windows to a deep subsurface biosphere. We conclude that the deep-sea extremophiles are very closely related into the unseen majority in subsurface biosphere, and the subsurface biosphere probably concerns to consider the "exobiology".     

Impact constraints on the environment for chemical evolution and the continuity of life

The Moon and the Earth were bombarded heavily by planetesimals and asteroids that were capable of interfering with chemical evolution and the origin of life. In this paper, we explore the frequency of giant terrestrial impacts able to stop prebiotic chemistry in the probable regions of chemical evolution. The limited time available between impacts disruptive to prebiotic chemistry at the time of the oldest evidence of life suggests the need for a rapid process for chemical evolution of life. The classical hypothesis for the origin of life through the slow accumulation of prebiotic reactants in the primordial soup in the entire ocean may not be consistent with constraints imposed by the impact history of Earth. On the other hand, rapid chemical evolution in cloud systems and lakes or other shallow evaporating water bodies would have been possible because reactants could have been concentrated and polymerized rapidly in this environment. Thus, life probably could have originated near the surface between frequent surface sterilizing impacts. There may not have been continuity of life depending on sunlight because there is evidence that life, existing as early as 3.8 Gyr ago, may have been destroyed by giant impacts. The first such organisms on Earth where probably not the ancestors of present life.     

Human optokinetic responses under quasi-open and closed loop conditions

The human optokinetic response to a horizontally moving striped pattern surrounding the subject was investigated under quasi-open and closed loop conditions. Open loop conditions were produced by the addition of an external signal from measured slow phase eye velocity to stripe velocity. A comparison of open and closed loop responses to step and sinusoidal changes of stripe velocity indicates that the central nervous system controlling slow phase optokinetic following can be described as a simple first order lag (Ka/(s+a)) where K is 4.7 and the time constant, 1/a, is 1.25 s.     

Hydrogen peroxide and the evolution of oxygenic photosynthesis

The early atmosphere of the Earth is considered to have been reducing (H₂ rich) or neutral (CO₂-N₂). The present atmosphere by contrast is highly oxidizing (20% O₂). The source of this oxygen is generally agreed to have been oxygenic photosynthesis, whereby organisms use water as the electron donor in the production of organic matter, liberating oxygen into the atmosphere. A major question in the evolution of life is how oxygenic photosynthesis could have evolved under anoxic conditions — and also when this capability evolved. It seems unlikely that water would be employed as the electron donor in anoxic environments that were rich in reducing agents such as ferrous or sulfide ions which could play that role. The abiotic production of atmospheric oxidants could have provided a mechanism by which locally oxidizing conditions were sustained within spatially confined habitats thus removing the available reductants and forcing photosynthetic organisms to utilize water as the electron donor. We suggest that atmospheric H₂O₂ played the key role in inducing oxygenic photosynthesis because as peroxide increased in a local environment, organisms would not only be faced with a loss of reductant, but they would also be pressed to develop the biochemical apparatus (e.g., catalase) that would ultimately be needed to protect against the products of oxygenic photosynthesis. This scenario allows for the early evolution of oxygenic photosynthesis while global conditions were still anaerobic.     

Recent advances in petroleum microbiology.

Recent advances in molecular biology have extended our understanding of the metabolic processes related to microbial transformation of petroleum hydrocarbons. The physiological responses of microorganisms to the presence of hydrocarbons, including cell surface alterations and adaptive mechanisms for uptake and efflux of these substrates, have been characterized. New molecular techniques have enhanced our ability to investigate the dynamics of microbial communities in petroleum-impacted ecosystems. By establishing conditions which maximize rates and extents of microbial growth, hydrocarbon access, and transformation, highly accelerated and bioreactor-based petroleum waste degradation processes have been implemented. Biofilters capable of removing and biodegrading volatile petroleum contaminants in air streams with short substrate-microbe contact times (<60 s) are being used effectively. Microbes are being injected into partially spent petroleum reservoirs to enhance oil recovery. However, these microbial processes have not exhibited consistent and effective performance, primarily because of our inability to control conditions in the subsurface environment. Microbes may be exploited to break stable oilfield emulsions to produce pipeline quality oil. There is interest in replacing physical oil desulfurization processes with biodesulfurization methods through promotion of selective sulfur removal without degradation of associated carbon moieties. However, since microbes require an environment containing some water, a two-phase oil-water system must be established to optimize contact between the microbes and the hydrocarbon, and such an emulsion is not easily created with viscous crude oil. This challenge may be circumvented by application of the technology to more refined gasoline and diesel substrates, where aqueous-hydrocarbon emulsions are more easily generated. Molecular approaches are being used to broaden the substrate specificity and increase the rates and extents of desulfurization. Bacterial processes are being commercialized for removal of H(2)S and sulfoxides from petrochemical waste streams. Microbes also have potential for use in removal of nitrogen from crude oil leading to reduced nitric oxide emissions provided that technical problems similar to those experienced in biodesulfurization can be solved. Enzymes are being exploited to produce added-value products from petroleum substrates, and bacterial biosensors are being used to analyze petroleum-contaminated environments.     

Surface and subsurface nitrate flow pathways on a watershed scale

Determining the interaction and impact of surface runoff and subsurface flow processes on the environment has been hindered by our inability to characterize subsurface soil structures on a watershed scale. Ground penetrating radar (GPR) data were collected and evaluated in determining subsurface hydrology at four small watersheds in Beltsville, MD. The watersheds have similar textures, organic matter contents, and yield distributions. Although the surface slope was greater on one of the watersheds, slope alone could not explain why it also had a nitrate runoff flux that was 18 times greater than the other three watersheds. Only with knowledge of the subsurface hydrology could the surface runoff differences be explained. The subsurface hydrology was developed by combining GPR and surface topography in a geographic information system. Discrete subsurface flow pathways were identified and confirmed with color infrared imagery, real-time soil moisture monitoring, and yield monitoring. The discrete subsurface flow patterns were also useful in understanding observed nitrate levels entering the riparian wetland and first order stream. This study demonstrated the impact that subsurface stratigraphy can have on water and nitrate (NO3-N) fluxes exiting agricultural lands, even when soil properties, yield distributions, and climate are similar. Reliable protocols for measuring subsurface fluxes of water and chemicals need to be developed.     

Recent Advances in Petroleum Microbiology

Recent advances in molecular biology have extended our understanding of the metabolic processes related to microbial transformation of petroleum hydrocarbons. The physiological responses of microorganisms to the presence of hydrocarbons, including cell surface alterations and adaptive mechanisms for uptake and efflux of these substrates, have been characterized. New molecular techniques have enhanced our ability to investigate the dynamics of microbial communities in petroleum-impacted ecosystems. By establishing conditions which maximize rates and extents of microbial growth, hydrocarbon access, and transformation, highly accelerated and bioreactor-based petroleum waste degradation processes have been implemented. Biofilters capable of removing and biodegrading volatile petroleum contaminants in air streams with short substrate-microbe contact times (<60 s) are being used effectively. Microbes are being injected into partially spent petroleum reservoirs to enhance oil recovery. However, these microbial processes have not exhibited consistent and effective performance, primarily because of our inability to control conditions in the subsurface environment. Microbes may be exploited to break stable oilfield emulsions to produce pipeline quality oil. There is interest in replacing physical oil desulfurization processes with biodesulfurization methods through promotion of selective sulfur removal without degradation of associated carbon moieties. However, since microbes require an environment containing some water, a two-phase oil-water system must be established to optimize contact between the microbes and the hydrocarbon, and such an emulsion is not easily created with viscous crude oil. This challenge may be circumvented by application of the technology to more refined gasoline and diesel substrates, where aqueous-hydrocarbon emulsions are more easily generated. Molecular approaches are being used to broaden the substrate specificity and increase the rates and extents of desulfurization. Bacterial processes are being commercialized for removal of H₂S and sulfoxides from petrochemical waste streams. Microbes also have potential for use in removal of nitrogen from crude oil leading to reduced nitric oxide emissions provided that technical problems similar to those experienced in biodesulfurization can be solved. Enzymes are being exploited to produce added-value products from petroleum substrates, and bacterial biosensors are being used to analyze petroleum-contaminated environments.     

Metabolism and motility in prebiotic structures

Easily accessible, primitive chemical structures produced by self-assembly of hydrophobic substances into oil droplets may result in self-moving agents able to sense their environment and move to avoid equilibrium. These structures would constitute very primitive examples of life on the Earth, even more primitive than simple bilayer vesicle structures. A few examples of simple chemical systems are presented that self-organize to produce oil droplets capable of movement, environment remodelling and primitive chemotaxis. These chemical agents are powered by an internal chemical reaction based on the hydrolysis of an oleic anhydride precursor or on the hydrolysis of hydrogen cyanide (HCN) polymer, a plausible prebiotic chemistry. Results are presented on both the behaviour of such droplets and the surface-active properties of HCN polymer products. Such motile agents would be capable of finding resources while escaping equilibrium and sustaining themselves through an internal metabolism, thus providing a working chemical model for a possible origin of life.     

Two possible conducting states of the influenza A virus M2 ion channel

Molecular dynamics simulations have been performed on protonated four-helix bundles based on the 25-residue Duff-Ashley transmembrane sequence of the M2 channel of the influenza A virus. Well-equilibrated tetrameric channels, with one, two and four of the H37 residues protonated, were investigated. The protonated peptide bundles were immersed in the octane portion of a phase-separated water/octane system, which provided a membrane-mimetic environment. The simulations suggest that there could be two conducting states of the M2 channel corresponding to tetramers containing one or two protonated histidines. The more open structure of the doubly protonated state suggests it would have the higher conductance.     

Thermal Energy and the Origin of Life

Life has evolved on Earth with electromagnetic radiation (light), fermentable organic molecules, and oxidizable chemicals as sources of energy. Biological use of thermal energy has not been observed although heat, and the thermal gradients required to convert it into free energy, are ubiquitous and were even more abundant at the time of the origin of life on Earth. Nevertheless, Earth-organisms sense thermal energy, and in suitable environments may have gained the capability to use it as energy source. It has been proposed that the first organisms obtained their energy by a first protein named pF₁ that worked on a thermal variation of the binding change mechanism of today's ATP sythase enzyme. Organisms using thermosynthesis may still live where light or chemical energy sources are not available. Possible suitable examples are subsurface environments on Earth and in the outer Solar System, in particular the subsurface oceans of the icy satellites of Jupiter and Saturn.     

Role of aromatic localization in the gating process of a potassium channel

Position of the transmembrane aromatic residues of the KirBac1.1 potassium channel shifts from an even distribution in the closed state toward the membrane/solute interface in the open state model. This is the first example of an integral membrane protein making use of the observed preference for transmembrane aromatic residues to reside at the interfaces. The process of aromatic localization is proposed as a means of directing and stabilizing structural changes during conformational transitions within the transmembrane region of integral membrane proteins. All-atom molecular dynamics simulations of the open and closed conformers in a membrane environment have been carried out to take account of the interactions between the aromatic residues and the lipids, which may be involved in the conformational change, e.g., the gating of the channel.     

Role of Aromatic Localization in the Gating Process of a Potassium Channel

Position of the transmembrane aromatic residues of the KirBac1.1 potassium channel shifts from an even distribution in the closed state toward the membrane/solute interface in the open state model. This is the first example of an integral membrane protein making use of the observed preference for transmembrane aromatic residues to reside at the interfaces. The process of aromatic localization is proposed as a means of directing and stabilizing structural changes during conformational transitions within the transmembrane region of integral membrane proteins. All-atom molecular dynamics simulations of the open and closed conformers in a membrane environment have been carried out to take account of the interactions between the aromatic residues and the lipids, which may be involved in the conformational change, e.g., the gating of the channel.     

Isotonic Water Transport in Secretory Epithelia ,

The model proposed by Diamond and Bossert [1] for isotonic water transport has received wide acceptance in recent years. It assumes that the local driving force for water transport is a standing osmotic gradient produced in the lateral intercellular spaces of the epithelial cell layer by active solute transport. While this model is based on work done in absorptive epithelia where the closed to open direction of the lateral space and the direction of net transport are the same, it has been proposed that the lateral spaces could also serve as the site of the local osmotic gradients for water transport in secretory epithelia, where the closed to open direction of the lateral space and net transport are opposed, by actively transporting solute out of the space rather than into it. Operation in the backward direction, however, requires a lower than ambient hydrostatic pressure within the lateral space which would seem more likely to cause the space to collapse with loss of function. On the other hand, most secretory epithelia are characterized by transport into a restricted ductal system which is similar to the lateral intercellular space in the absorptive epithelia in that its closed to open direction is the same as that of net transport. In vitro micropuncture studies on the exocrine pancreas of the rabbit indicate the presence of a small but statistically significant increase in juice osmolality, 6 mOsm/kg H₂O, at the site of electrolyte and water secretion in the smallest extralobular ducts with secretin stimulation which suggests that the ductal system in the secretory epithelia rather than the lateral intercellular space is the site of the local osmotic gradients responsible for isotonic water transport.