Genomic potential hypothesis of evolution: a concept of biogenesis in habitable spaces of the universe.
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The new hypothesis of evolution establishes a contiguity of life sciences with cosmology, physics, and chemistry, and provides a basis for the search for life on other planets. Chemistry is the sole driving force of the assembly of life, under the subtle guidance exerted by bonding orbital geometry. That phenomenon leads to multiple origins that function on the same principles but are different to the extent that their nucleic acid core varies. Thus, thoughts about the origins of life and the development of complexity have been transferred from the chance orientation of the past to the realm of atomic structures, which are subject to the laws of thermodynamics and kinetics. Evolution is a legitimate subject of basic science, and the complexity of life will submit to the laws of chemistry and physics as the problem is viewed from a new perspective. The paradigm connects life to the big events that formed every sphere of our living space and that keeps conditions fine-tuned for life to persist, perhaps a billion years or more. The "genomic potential" hypothesis leads to the prediction that life like ours is likely to exist in galaxies that are as distant from the origin of the universe as the Milky Way, and that the habitable zone of our galaxy harbors other living planets as well. (+info)
Molecular indicators (biomarkers) of past life.
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Biomarkers in geological samples on Earth are products derived from biochemical precursors (i.e., natural products) by reductive and oxidative alteration processes (e.g., cholestanes from cholesterol). Generally, lipids, pigments, and some biomembranes are preserved best over longer geological times, and labile compounds such as amino acids, sugars, etc. are useful biomarkers for recent times. Thus, the detailed characterization of biomarker composition permits the assessment of the major contributing species of extinct and/or extant life. Nonbiomarkers and abiogenic organic compounds are also discussed. In the case of the early Earth, work has progressed to elucidate biomarker structures and carbon isotopic signals preserved in ancient sedimentary rocks. In addition, the combination of bacterial biochemistry with the organic geochemistry of contemporary and ancient hydrothermal ecosystems permits the modeling of the nature, behavior, and preservation potential of primitive microbial communities. This approach entails combined molecular and isotopic analyses to characterize lipids and biopolymers produced by cultured bacteria (representative of ancient strains) and to test a variety of culture conditions that affect their biosynthesis processes. In regards to Mars, the biomarkers from lipids and biopolymers would be expected to be preserved best if life flourished there during its early history (3.5-4 x 10(9) years ago). Both oxidized and reduced products would be expected. This is based on the inference that hydrothermal activity occurred during that time, with the concomitant preservation of biochemically-derived carbonaceous matter. Known biomarkers (i.e., as elucidated for early terrestrial samples and for primitive terrestrial microbiota) as well as novel, potentially unknown compounds, should be characterized. (+info)
Membrane self-assembly processes: steps toward the first cellular life.
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This review addresses the question of the origin of life, with emphasis on plausible boundary structures that may have initially provided cellular compartmentation. Some form of compartmentation is a necessary prerequisite for maintaining the integrity of interdependent molecular systems that are associated with metabolism, and for permitting variations required for speciation. The fact that lipid-bilayer membranes define boundaries of all contemporary living cells suggests that protocellular compartments were likely to have required similar, self-assembled boundaries. Amphiphiles such as short-chain fatty acids, which were presumably available on the early Earth, can self-assemble into stable vesicles that encapsulate hydrophilic solutes with catalytic activity. Their suspensions in aqueous media have therefore been used to investigate nutrient uptake across simple membranes and encapsulated catalyzed reactions, both of which would be essential processes in protocellular life forms. (+info)
Toward the engineering of minimal living cells.
(20/112)
The article focuses on the notion of a synthetic or semi-synthetic minimal cell, defined as a system that has the minimal and sufficient structural conditions for cellular life. It is emphasized that two complementary approaches are in principle possible, defined as "bottom-up" and "top-down" approaches. The first one aims at the construction of a minimal cell starting from scratch, and it is argued that a very serious bottle-neck to this pathway lies in the origination of specific macro-molecular sequences, as in nature those were constructed most likely by a particular contingent set of conditions. The top-down approaches utilize extant genes and enzymes, and the work in this case is based on the incorporation of the minimal and sufficient amount of such macromolecules into liposomes, as models for the shell of biological cells. The first phase of this ambitious project foresees the study of conditions under which complex molecular biology reactions takes place in the compartments of liposomes. Examples of these reactions are provided, for example, the production of RNA throughout Q-beta replicase in a self-reproducing vesicle system; or PC Reaction in phospholipid vesicles; or even the incorporation of ribosomes in liposomes, with the production of polypeptide chains. The use of giant vesicles is also illustrated. These systems, due to their large size, offer the advantage that by way of special micro-injection techniques, all sort of biochemical agents can be directly introduced in the compartment; and that the reaction can be followed by optical microscopy. In the final part of the article, the outlook of increasing the complexity of these liposome systems so as to arrive at first semi-synthetic cells is discussed. (+info)
How did cells get their size?
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Cells exercise size homeostasis, and the origins of their ability to do so is the topic of this essay. Before there were cells, there were protocells. The most basic questions about protocells as objects are: What were they made of, and how big were they? Asking how big they were implies that the answer to the first part includes a boundary. The best candidate for that boundary is a self-assembling lipid bilayer. Therefore, protocells are defined here as Darwinian liposomes-bilayer vesicles with mutable on-board replicases linked to phenotypes. Because liposomes undergo spontaneous fission and fusion, and are subject to osmotic forces, size regulation in the earliest protocells would essentially have been liposome physics. For successful protocells, averting osmotic lysis would have been the first order of business. However, from the outset size mattered too, because of sex and reproduction (i.e., genome mixing and genome copying in entities with phenotypes). Protocell fission and fusion would have blended seamlessly into protocell sex and reproduction, making any gene product that furnished control over protocell size changes doubly adaptive. A recurrent theme is the feedback role of bilayer tension in protocell size control. Ways in which primitive peptides and their aggregates (e.g., channels) might have allowed liposomes to gain improved volume and surface area homeostasis are suggested. Domain-swapped proteins that polymerize as filaments are discussed as the origin of cytoskeleton structures that diversify and stabilize liposome shapes and sizes. Throughout, attention is paid to the question of set points for cell size. (+info)
Prebiotic synthesis from CO atmospheres: implications for the origins of life.
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Most models of the primitive atmosphere around the time life originated suggest that the atmosphere was dominated by carbon dioxide, largely based on the notion that the atmosphere was derived via volcanic outgassing, and that those gases were similar to those found in modern volcanic effluent. These models tend to downplay the possibility of a strongly reducing atmosphere, which had been thought to be important for prebiotic synthesis and thus the origin of life. However, there is no definitive geologic evidence for the oxidation state of the early atmosphere and bioorganic compounds are not efficiently synthesized from CO(2) atmospheres. In the present study, it was shown that a CO-CO(2)-N(2)-H(2)O atmosphere can give a variety of bioorganic compounds with yields comparable to those obtained from a strongly reducing atmosphere. Atmospheres containing carbon monoxide might therefore have been conducive to prebiotic synthesis and perhaps the origin of life. CO-dominant atmospheres could have existed if the production rate of CO from impacts of extraterrestrial materials were high or if the upper mantle had been more reduced than today. (+info)
Demystified. Nitric oxide.
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The discovery of nitric oxide (NO) demonstrated that cells could communicate via the manufacture and local diffusion of an unstable lipid soluble molecule. Since the original demonstration of the vascular relaxant properties of endothelium derived NO, this fascinating molecule has been shown to have multiple, complex roles within many biological systems. This review cannot hope to cover all of the recent advances in NO biology, but seeks to place the discovery of NO in its historical context, and show how far our understanding has come in the past 20 years. The role of NO in mitochondrial respiration, and consequently in oxidative stress, is described in detail because these processes probably underline the importance of NO in the development of disease. (+info)
Kinetics and activation parameter analyses of hydrolysis and interconversion of 2',5'- and 3',5'-linked dinucleoside monophosphate at extremely high temperatures.
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Kinetic analysis of hydrolytic stability of 2',5'- and 3',5'-linked dinucleoside monophosphate (N(2)'pN and N(3)'pN) was successfully performed in aqueous solution at 175-240 degrees C using a new real-time monitoring method for rapid hydrothermal reactions. The half-lives of NpN were in the range 2-8 s at 240 degrees C and apparent activation energy decreases in the order U(2)'pU>A(2)'pA>G(2)'pG>U(3)pU approximately C(3)'pC>A(3)pA. The stability of phosphodiester bond was dependent on the types of base moiety and phosphodiester linkages, but no systematic correlation was found between the structure and stability. The interconversion of 2',5'-adenylyladenosine monophosphate (A(2)'pA) and 3',5'-adenylyladenosine monophosphate (A(3)'pA) was enhanced in the presence of D- or L-histidine. The rate constants of degradation of NpN were dissected into the rate constants of hydrolysis and interconversion between N(2)'pN and N(3)'pN using a computer program SIMFIT. Kinetic analysis supports the mechanism that imidazolium ion and imidazole catalyze interconversion and hydrolysis even under hydrothermal environments. The activation parameters for the hydrolysis and interconversion of NpN were systematically determined for the first time from the temperature dependence of the rate constants, where both DeltaH(app)( not equal ) and DeltaS(app)( not equal ) for 2',5'-linked NpN are larger than those for 3',5'-linked NpN. These parameters support the pseudorotation mechanism through pentacoordinate intermediate from 2',5'- and 3',5'-linked NpN, where the average value of DeltaH( not equal ) (pseudorotation) was estimated to be 30+/-18 kJ mol(-1) at 175-240 degrees C. (+info)