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PubMed1998

Power measurements of spark discharge experiments.

An accurate and precise knowledge of the amount of energy introduced into prebiotic discharge experiments is important to understand the relative roles of different energy sources in the synthesis of organic compounds in the primitive Earth's atmosphere and other planetary atmospheres. Two methods widely used to determine the power of spark discharges were evaluated, namely calorimetric and oscilloscopic, using a chemically inert gas. The power dissipated by the spark in argon at 500 Torr was determined to be 2.4 (+12%/-17%) J s-1 by calorimetry and 5.3 (+/- 15%) J s-1 by the oscilloscope. The difference between the two methods was attributed to (1) an incomplete conversion of the electric energy into heat, and (2) heat loss from the spark channel to the connecting cables through the electrodes. The latter contribution leads to an unwanted effect in the spark channel by lowering the spark product yields as the spark channel cools by mixing with surrounding air and by losing heat to the electrodes. Once the concentrations of the spark products have frozen at the freeze-out temperature, any additional loss of heat from the spark channel to the electrodes has no consequence in product yields. Therefore, neither methods accurately determines the net energy transferred to the system. With a lack of a quantitative knowledge of the amount of heat loss from the spark channel during the interval from ignition of the spark to when the freeze-out temperature is reached, it is recommended to derive the energy yields of the spark products from the mean value of the two methods with the uncertainty being their standard deviation. For the case of argon at 500 Torr, this would be 3.8 (+/-50%) J s-1.

Argon↗
PubMed2002

Chemical constraints governing the origin of metabolism: the thermodynamic landscape of carbon group transformations under mild aqueous conditions.

The thermodynamics of organic chemistry under mild aqueous conditions was examined in order to begin to understand its influence on the structure and operation of metabolism and its antecedents. Free energies (deltaG) were estimated for four types of reactions of biochemical importance carbon-carbon bond cleavage and synthesis, hydrogen transfer between carbon groups, dehydration of alcohol groups, and aldo-keto isomerization. The energies were calculated for mainly aliphatic groups composed of carbon, hydrogen, and oxygen. The energy values showed (1) that generally when carbon-carbon bond cleavage involves groups from different functional group classes (i.e., carboxylic acids, carbonyl groups, alcohols, and hydrocarbons), the transfer of the shared electron-pair to the more reduced carbon group is energetically favored over transfer to the more oxidized carbon group, and (2) that the energy of carbon-carbon bond transformation is primarily determined by the functional group class of the group that changes oxidation state in the reaction (i.e., the functional group class of the group that donates the shared electron-pair during cleavage, or that accepts the incipient shared electron-pair during synthesis). In contrast, the energy of hydrogen transfer between carbon groups is determined by the functional group class of both the hydrogen-donor group and the hydrogen-acceptor group. From these and other observations we concluded that the chemistry involved in the origin of metabolism (and to a lesser degree modern metabolism) was strongly constrained by (1) the limited redox-based transformation energy of organic substrates that is readily dissipated in a few energetically favorable irreversible reactions; (2) the energy dominance of a few transformation half-reactions that determines whether carbon-carbon bond transformation (cleavage or synthesis) is energetically favorable (deltaG < -3.5 kcal/mol), reversible (deltaG between +/-3.5 kcal/mol), or unfavorable (deltaG > +3.5 kcal/mol); and (3) the dependence of carbon group transformation energy on the functional group class (i.e., oxidation state) of participating groups that in turn is contingent on prior reactions and precursors in the synthetic pathway.

Carbon↗
PubMed2005

Life begins.

Explore the source record for details and available documents.

Art↗
PubMed1992

Proton magnetic resonance spectroscopic imaging for metabolic characterization of demyelinating plaques.

We used proton magnetic resonance (MR) spectroscopic imaging to determine the serial changes in MR signals from choline, creatine, lactate, and N-acetylaspartate in and around a large demyelinating lesion followed over a period of 8 months. Elevated lactate and choline signals were observed at the first examination 3 days after the onset of symptoms. Reduced N-acetylaspartate signals were observed a few days afterward. The abnormal metabolite signals varied in different regions of the lesion and extended beyond the borders of abnormal signal intensity seen on conventional MR imaging (MRI). On the last examination at 8 months when the lesion appeared much smaller on MRI, choline signals from the center of the lesion were still high, but were falling. Choline signals outside the lesion on MRI had returned to normal as had lactate signals everywhere. Importantly, there was no recovery of N-acetylaspartate signals in or adjacent to the lesion on MRI. This serial study demonstrates the potential of MR spectroscopic imaging for characterizing the chemical pathological evolution of demyelinating lesions in ways that conventional MRI cannot. We propose that abnormal signals from choline can indicate recent regional demyelination, while persistent abnormal signals from N-acetylaspartate can provide an index of irreversible damage in the nervous system.

Acute Disease↗
PubMed2002

Genomic potential hypothesis of evolution: a concept of biogenesis in habitable spaces of the universe.

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.

Biological Evolution↗
PubMed2002

Molecular indicators (biomarkers) of past life.

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.

Bacterial Physiological Phenomena↗
PubMed2002

Membrane self-assembly processes: steps toward the first cellular life.

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.

Biological Evolution↗
PubMed2002

Toward the engineering of minimal living cells.

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.

Biopolymers↗
PubMed2002

How did cells get their size?

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.

Biological Evolution↗
PubMed2004

Exploratory studies to investigate a linked prebiotic origin of RNA and coded peptides. 3rd communication. Behaviour of 5-amino-1H-imidazole-4-carbonitrile derivatives.

The potentially prebiotic synthesis of pyrimidine ribonucleotides by stepwise nucleobase assembly on arabinose-3-phosphate derivatives has been demonstrated in previous work. The generation of xylose-2-phosphate derivatives by aldolisation, and the behaviour of these compounds under the conditions of pyrimidine nucleobase assembly have also been described. In this paper, the scope for generation of purine nucleotides via 3,3'-anhydro-xylo-nucleotides is investigated. In neutral D2O solution, the potential intermediate 47 (Schemes 6 and 8) undergoes H-C2 --> D-C2 exchange, but no appreciable reaction with cyanide or cyanamide occurs. The exchange chemistry expands options for purine nucleobase assembly on sugar phosphate scaffolds.

Evolution, Chemical↗
PubMed2004

Multiple aromaticity and antiaromaticity in silicon clusters.

A series of silicon clusters containing four atoms but with different charge states (Si4(2+), Si4, Si4(2-), and NaSi4-) were studied by photoelectron spectroscopy and ab initio calculations. Structure evolution and chemical bonding in this series were interpreted in terms of aromaticity and antiaromaticity, which allowed the prediction of how structures of the four-atom silicon clusters change upon addition or removal of two electrons. It is shown that Si4(2+) is square-planar, analogous to the recently discovered aromatic Al4(2-) cluster. Upon of two electrons, neutral Si4 becomes sigma-antiaromatic and exhibits a rhombus distortion. Adding two more electrons to Si4 leads to two energetically close structures of Si4(2-): either a double antiaromatic parallelogram structure or an aromatic system with a butterfly distortion. Because of the electronic instability of doubly charged Si4(2-), a stabilizing cation (Na+) was used to produce Si4(2-) in the gas phase in the form of Na+[Si4(2-)], which was characterized experimentally by photoelectron spectroscopy. Multiple antiaromaticity in the parallelogram Na+[Si4(2-)] species is highly unusual.

Journal Article↗
PubMed2005

Ultrafast electron diffraction: dynamical structures on complex energy landscapes.

In this contribution, we report studies in ultrafast electron diffraction (UED), with the aim of exploring new directions. The main focus is on the determination of complex structures and their dynamics with spatial and temporal resolutions sufficient to give an atomic-scale picture for the evolution in chemical or biological change. We also provide the theoretical framework for UED, and compare the experimental findings of UED to those predicted by density functional and charge density calculations. Selected applications are given in order to highlight phenomena related to concepts such as bifurcation of trajectories in dynamics, far-from-equilibrium coherent structures, and conformational robustness in biological structures. For the former two cases, we consider chemical systems, and, for the latter, we examine proteins of 200 atoms (angiotensin I) or more.

Journal Article↗
PubMed2003

Vitamin D: A millenium perspective.

Vitamin D is one of the oldest hormones that have been made in the earliest life forms for over 750 million years. Phytoplankton, zooplankton, and most plants and animals that are exposed to sunlight have the capacity to make vitamin D. Vitamin D is critically important for the development, growth, and maintenance of a healthy skeleton from birth until death. The major function of vitamin D is to maintain calcium homeostasis. It accomplishes this by increasing the efficiency of the intestine to absorb dietary calcium. When there is inadequate calcium in the diet to satisfy the body's calcium requirement, vitamin D communicates to the osteoblasts that signal osteoclast precursors to mature and dissolve the calcium stored in the bone. Vitamin D is metabolized in the liver and then in the kidney to 1,25-dihydroxyvitamin D [1,25(OH)(2)D]. 1,25(OH)(2)D receptors (VDR) are present not only in the intestine and bone, but in a wide variety of other tissues, including the brain, heart, stomach, pancreas, activated T and B lymphocytes, skin, gonads, etc. 1,25(OH)(2)D is one of the most potent substances to inhibit proliferation of both normal and hyperproliferative cells and induce them to mature. It is also recognized that a wide variety of tissues, including colon, prostate, breast, and skin have the enzymatic machinery to produce 1,25(OH)(2)D. 1,25(OH)(2)D and its analogs have been developed for treating the hyperproliferative disease psoriasis. Vitamin D deficiency is a major unrecognized health problem. Not only does it cause rickets in children, osteomalacia and osteoporosis in adults, but may have long lasting effects. Chronic vitamin D deficiency may have serious adverse consequences, including increased risk of hypertension, multiple sclerosis, cancers of the colon, prostate, breast, and ovary, and type 1 diabetes. There needs to be a better appreciation of the importance of vitamin D for overall health and well being.

Adult↗