The prebiotic molecules observed in the interstellar gas

Over 130 molecules have been identified in the interstellar gas and circumstellar shells, the largest among them is a carbon chain with 13 atoms and molecular weight of 147 (twice that of the simplest amino acid glycine). The high reliability of astronomical identifications, as well as the fairly accurate quantitative analysis which can often be achieved, is emphasized. Glycine itself has been claimed, but a recent analysis indicates that few, if any, of the astronomical radio lines attributed to glycine are actually from that molecule. Polycyclic aromatic hydrocarbons (PAHs) have long been proposed as the source of the unidentified infrared bands between 3 and 16 microm, but no single PAH has been identified in space, partly because PAHs generally have weak or non-existent radio spectra. A remarkable exception is the non-planar corannulene molecule (C20H10) that has a strong radio spectrum; in the rich molecular cloud TMC-1, it is found that less than 10-5 of the carbon is contained in this molecule, suggesting that PAHs are not the dominant large molecules in the interstellar gas, as has been claimed. Owing to inherent spectroscopic limitations, determining the structures of the large molecules in space may require capture of the dust grains, which are continually entering the outer Solar System.     

Analysis and Prediction of the Critical Regions of Antimicrobial Peptides Based on Conditional Random Fields

Antimicrobial peptides (AMPs) are potent drug candidates against microbes such as bacteria, fungi, parasites, and viruses. The size of AMPs ranges from less than ten to hundreds of amino acids. Often only a few amino acids or the critical regions of antimicrobial proteins matter the functionality. Accurately predicting the AMP critical regions could benefit the experimental designs. However, no extensive analyses have been done specifically on the AMP critical regions and computational modeling on them is either non-existent or settled to other problems. With a focus on the AMP critical regions, we thus develop a computational model AMPcore by introducing a state-of-the-art machine learning method, conditional random fields. We generate a comprehensive dataset of 798 AMPs cores and a low similarity dataset of 510 representative AMP cores. AMPcore could reach a maximal accuracy of 90% and 0.79 Matthew’s correlation coefficient on the comprehensive dataset and a maximal accuracy of 83% and 0.66 MCC on the low similarity dataset. Our analyses of AMP cores follow what we know about AMPs: High in glycine and lysine, but low in aspartic acid, glutamic acid, and methionine; the abundance of α-helical structures; the dominance of positive net charges; the peculiarity of amphipathicity. Two amphipathic sequence motifs within the AMP cores, an amphipathic α-helix and an amphipathic π-helix, are revealed. In addition, a short sequence motif at the N-terminal boundary of AMP cores is reported for the first time: arginine at the P(-1) coupling with glycine at the P1 of AMP cores occurs the most, which might link to microbial cell adhesion.     

Photochemical conversions of lower aldehydes in aqueous solutions and in fog

One of the possible paths of abiogenic synthesis of biologically important compounds on primordial Earth, as well as under extraterrestrial conditions, might have been the photochemical conversions of polyatomic organic molecule detected at present in the interstellar medium and in cosmic bodies. The important contribution from lower aldehydes is emphasized. Experimental results show that amino acids, peptide-like compounds, N-heterocyclic compounds, etc., are formed by UV irradiation (254 nm) of aqueous solutions either of formaldehyde, or of acetaldehyde with ammonium nitrate. UV-irradiated fog of the same composition yields aminoacids, mostly glycine.     

The occurrence of glycine in bacterial lipopolysaccharides

Abstract The aminoacyl analysis of endotoxic lipopolysaccharides (LPS) isolated from several bacteria revealed essential amounts of glycine, among the inherent LPS components. Significant amounts of the glycine was detected in lipopolysaccharides isolated from over 30 strains of Escherichia, Salmonella, Hafnia, Citrobacter and Shigella species. Glycine as a single amino acid was found only in a core part of LPS. Molar ratio of glycine in core oligosaccharide fraction ranged from 0.2 to 0.6 per 3 heptoses. The oligosaccharide enriched in glycine was isolated using the HPLC. The amino acid appeared to be terminally located in a core oligosaccharide. The labelling of the lipopolysaccharide cores was achieved when the bacteria were cultivated in the presence of radioactive [¹⁴C]glycine. The labelled core oligosaccharide released the radioactivity during treatment with mild alkali or acid (0.1 M NaOH or HCl, 100°C, 4 h). The radioactivity in SDS-polyacrylamide gel electrophoresis migrated exclusively with LPS. The results indicate that amino acid is an integral constituent of core oligosaccharide in lipopolysaccharide.     

Primary Sources of Phosphorus and Phosphates in Chemical Evolution

In this work we consider the role of phosphorus in chemical evolution from an interdisciplinary approach. First we briefly review the presence of this element in different cosmic sites, such as massive stellar cores, circumstellar and interstellar clouds, meteorites, lunar and Martian samples, interplanetary dust particles, cometary dust and planetary atmospheres. Thus we illustrate the fact that phosphorus seems to be, at the same time, scarce and ubiquitous in the solar system. Afterwards, by comparing the phosphorus content of our planet's main reservoirs with the amount of cometary and meteoritic matter captured by the primitive Earth, we conclude that comets may have provided a primary source for phosphorus compounds of prebiotic interest. Finally, we make a number of proposals aimed to gain observational supporting evidence to the above conclusion and other suggestions made in the article.     

Membrane-microfilament interactions in ascites tumor cell microvilli. Identification and isolation of a large microfilament-associated membrane glycoprotein complex

[14C]Glucosamine metabolic labeling and concanavalin A blots were used to identify four major glycoprotein species associated with ascites tumor cell microvillar microfilament cores and with a transmembrane complex containing actin. Phalloidin shift analysis of glucosamine-labeled microvilli showed that glycoproteins of 110-120, 80, 65, and 55 kDa are stably associated with the microfilament cores. Analysis of large (greater than 10(6) kDa) transmembrane complexes from microvillar membranes made under microfilament-depolymerizing conditions (Carraway, C. A. C., Jung, G., and Carraway, K. L. (1983) Proc. Natl. Acad. Sci. U. S. A. 80, 430-434) revealed glycoproteins of the same Mr values, showing the same relative staining or labeling patterns as those observed with the microfilament cores. Gel filtration of high salt, high pH extracts of intact microvilli, microfilament cores, or transmembrane complexes showed that in all of these fractions the glycoproteins are associated in a very large, stable complex. The glycoprotein multimer was isolated essentially free of actin and other components by Sephacryl S-1000 chromatography of microvilli, microvillar membranes prepared at pH 11, microfilament cores, or transmembrane complex fractions in Triton X-100, 1 M KCl, glycine, pH 9.5. Purified glycoprotein complex bound actin when incubated under polymerizing conditions. The presence of the glycoprotein heteromultimer in both microfilament cores and transmembrane complex from isolated membranes and the association of the purified glycoprotein complex with actin are consistent with our hypothesis that the glycoprotein-containing transmembrane complex is an association site for microfilaments at the plasma membrane.     

DETECTION OF ORGANIC MATTER IN INTERSTELLAR GRAINS

Star formation and the subsequent evolution of planetary systems occurs in dense molecular clouds, which are comprised, in part, of interstellar dust grains gathered from the diffuse interstellar medium (DISM). Radio observations of the interstellar medium reveal the presence of organic molecules in the gas phase and infrared observational studies provide details concerning the solid-state features in dust grains. In particular, a series of absorption bands have been observed near 3.4~2940 cm^–1) towards brightinfrared objects which are seen through large column densities of interstellar dust. Comparisons of organic residues, produced under a variety of laboratory conditions, to the diffuse interstellar medium observations have shown that aliphatic hydrocarbon grains are responsible for the spectral absorption features observed near 3.4 ~2940cm^–1). These hydrocarbons appear to carry the –CH₂– and –CH₃ functional groups in the abundance ratio CH₂/CH₃ ~ 2.5, and theamount of carbon tied up in this component is greater than 4% of the cosmic carbon available. On a galacticscale, the strength of the 3.4 band does notscale linearly with visual extinction, but instead increases more rapidly for objects near the Galactic Center. A similar trend is noted in the strength of the Si–O absorption band near 9.7. The similarbehavior of the C–H and Si–O stretching bands suggests that these two components may be coupled, perhaps in the form of grains with silicate cores and refractory organic mantles. The ubiquity of the hydrocarbon features seen in the near infrared near 3.4throughout our Galaxy and in other galaxies demonstrates the widespread availability of such material for incorporation into the many newly forming planetary systems. The similarity of the 3.4features in any organic material with aliphatic hydrocarbons underscores the need for complete astronomical observational coverage in the 2–30 region, oflines of sight which sample dust in both dense and diffuse interstellar clouds, in order to uniquely specify the composition of interstellar organics. This paper reviews the information available from ground-based observations, although currently the Infrared Satellite Observatory is adding to our body of knowledge on this subject by providing more extensive wavelength coverage. The Murchison carbonaceous meteorite has also been used as an analog to the interstellar observations and has revealed a striking similarity between the light hydrocarbons in the meteorite and the ISM; therefore this review includes comparisons with the meteoritic analog as well as with relevant laboratory residues. Fundamental to the evolution of the biogenic molecules, to the process of planetary system formation, and perhaps to the origin of life, is the connection between the organic material found in the interstellar medium and that incorporated in the most primitive solar system bodies.     

Natural abundance carbon-13 nuclear magnetic resonance studies of histone and DNA dynamics in nucleosome cores

Natural abundance carbon-13 nuclear magnetic resonance spectra (67.9 MHz) were obtained for native nucleosome cores: cores dissociated in 2 M NaCl and 2 M NaCl, 6 M urea; and cores degraded with DNase I plus proteinase K. Phosphorus-31 NMR spectra of native and dissociated cores and core length DNA were also obtained at 60.7 MHz. The 31P resonance and spin-lattice relaxation time (T1) of DNA were only slightly affected by packaging in nucleosome cores, in agreement with other reports, but 13C resonances of DNA were essentially unobservable. The loss of DNA spectral intensity suggests that rapid internal motions of DNA sugar carbons in protein-free DNA previously demonstrated by 13C NMR methods are partly restricted in nucleosomes. The 13C spectrum of native cores contains many narrow intense resonances assigned to lysine side chain and alpha-carbons, glycine alpha-carbons, alanine alpha- and beta- carbons, and arginine side chain carbons. Several weaker resonances were also assigned. The narrow line widths, short T1 values, and non-minimal nuclear Overhauser enhancements of these resonances, including alpha- and beta-carbons, show that some terminal chain segments of histones in nucleosomes are as mobile as small random coil polypeptides. The mobile segments include about 9% of all histone residues and 25% of all lysines, but only 10% of all arginines. The compositions of these segments indicate that mobile regions are located in amino- or carboxyl-terminal sequences of two or more histones. In addition, high mobility was observed for side chain carbons of 45-50% of all lysines (delta and epsilon carbons) and about 25% of all arginines (zeta carbon) in histones (including those in mobile segments), suggesting that basic residues in terminal histone sequences are not strongly involved in nucleosome structure and may instead help stabilize higher order chromatin structure.     

Chemical evolution in space

The bulk of complex molecules in the space between the stars is probably contained in small frozen interstellar dust grains. A typical grain is about as old as the earth and has, as a result of photochemical processing, converted a large fraction of its oxygen, carbon and nitrogen bearing mantle into large organic molecules whose maximum molecular weights are limited only by the grain size of about 0.1 m. Laboratory and theoretical methods provide the basis for explaining the evolution of interstellar grains from the time they are formed as seedlings in the atmospheres of cool evolved stars to the time they are destroyed by being incorporated into the material of new stars. The organic dust constitutes about one tenth of a percent of the total mass of the Milky Way and far outweighs any estimates of the total mass of all the planets. A planet like the earth is continually and directly accreting interstellar dust from space. Primitive carbonaceous meteorites show evidence of containing interstellar dust. Since comets are possibly almost pure aggregated interstellar dust they also provide a source of interstellar organic material on the earth.     

Interstellar molecules

Summary The study of interstellar molecules broadly includes two areas of interest. One area uses the unique ability of molecules to act as probes of the physical conditions in the cold, dense, visually opaque component of the interstellar medium. The physical properties of this and other components of the interstellar medium are summarized. The other area deals with the chemistry of interstellar molecules, recent aspects of which are emphasized in this review. Gas-phase chemistry, shock chemistry, and grain surface chemistry are discussed in the context of recent observations. No present observations suggest that surface reactions are relevant, but neither can they be ruled out. Ion-molecule reactions are clearly operative, at least for the simpler species. Chemical isotope fractionation is reviewed, andd it is concluded that the complexities of the chemistry allow no cosmological conclusions to be drawn from observations of deuterium in interstellar molecules, while the presence of¹³C in interstellar molecules permits an estimate of the¹²C/¹³C ratio which is consistent with the current concepts of the nucleosynthesis history of the Galaxy. Possible connections between interstellar molecules and the early molecular history of the solar system are discussed.This is the first of a series of papers which will appear in the Synthesis section of the Journal of Molecular Evolution pertaining to the topic Organic Molecules in the Solar System and Beyond.Operated by Associated Universitites, Inc., under contract with the National Science Foundation     

Maximum Number of Habitable Planets at the Time of Earth's Origin: New Hints for Panspermia?

New discoveries have fuelled the ongoing discussion of panspermia, i.e. the transport of life from one planet to another within the solar system (interplanetary panspermia) or even between different planetary systems (interstellar panspermia). The main factor for the probability of interstellar panspermia is the average density of stellar systems containing habitable planets. The combination of recent results for the formation rate of Earth-like planets with our estimations of extrasolar habitable zones allows us to determine the number of habitable planets in the Milky Way over cosmological time scales. We find that there was a maximum number of habitable planets around the time of Earth's origin. If at all, interstellar panspermia was most probable at that time and may have kick-started life on our planet.     

On the formation and observation of complex interstellar molecules

As of the present, a significant number of small molecules have been discovered in the interstellar medium. The largest molecule unambiguously detected, HC₁₁N, has only thirteen atoms. In this article, the prospects for observing far more complex species than this in interstellar clouds are discussed as are the mechanisms by which such complex species might be synthesized.     

Structure-function relationships in the ribosomal protein L12 in the archaeon Sulfolobus acidocaldarius.

A series of mutant L12 ribosomal proteins was prepared by site-directed mutations in the L12 protein gene of the archaeon Sulfolobus acidocaldarius. The mutant protein genes were overexpressed in Escherichia coli, and the products purified and incorporated into ribosomal cores which had been ethanol extracted to remove wild-type L12 protein. Measurements were made to determine if the mutation affected the binding of the L12 protein to the ribosome core or affected the translational activity of the resulting ribosome. Changing tyrosine [3] or tyrosine [5], conserved in all archaea and present in all eukarya in positions [3] and [7], to phenylalanine had no effect on binding or translational activity while changes to glycine significantly reduced binding and translational activity. Changing the single arginine [37] residue, conserved in almost all archaeal and eukaryal L12 proteins, to lysine, glutamic acid, glutamine, or glycine had no effect on binding to the core and had little or no significant effect on translational activity. The same was true when lysine [39], conserved in all archaeal L12 proteins, was changed to arginine, glutamic acid, glutamine, or glycine. Changing phenylalanine [104], the penultimate amino acid at the C-terminal end, which is conserved in all archaeal and eukaryal L12 proteins, to tyrosine or glycine had no effect on binding but lowered the translational activity by 60 and 75%, respectively, suggesting that this amino acid plays an important role in translation. Deletion of the highly charged region in the C-terminal domain, which is present in all archaeal and eukaryal L12 proteins, decreased transitional activity by 50%, suggesting this region is also involved in factor interactions.     

Isolation of Low-Molecular-Weight Proteins from Amyloid Plaque Fibers in Alzheimer''s Disease

During aging of the human brain, and particularly in Alzheimer's disease, progressive neuronal loss is accompanied by the formation of highly stable intra- and extraneuronal protein fibers. Using fluorescence-activated particle sorting, a method has been developed for purifying essentially to homogeneity the extracellular amyloid fibers that form the cores of senile plaques. The purified plaque cores each contain 60-130 pg of protein. Their amino acid composition shows abundant glycine, trace proline, and approximately 50% hydrophobic residues; it resembles that of enriched fractions of the paired helical filaments (PHF) that accumulate intraneuronally in Alzheimer's disease. Senile plaque amyloid fibers share with PHF insolubility in numerous protein denaturants and resistance to proteinases. However, treatment of either fiber preparation with concentrated (88%) formic acid or saturated (6.8 M) guanidine thiocyanate followed by sodium dodecyl sulfate causes disappearance of the fibers and releases proteins migrating at 5-7,000 and 11-15,000 Mr which appear to be dimerically related. Following their separation by size-exclusion HPLC, the proteins solubilized from plaque amyloid and PHF-enriched fractions have highly similar compositions and, on dialysis, readily aggregate into higher Mr polymers. Antibodies raised to the major low-Mr protein selectively label both plaque cores and vascular amyloid deposits in Alzheimer brain but do not stain neurofibrillary tangles, senile plaque neurites, or any other neuronal structure. Thus, extraneuronal amyloid plaque filaments in Alzheimer's disease are composed of hydrophobic low-Mr protein(s) which are also present in vascular amyloid deposits. Current evidence suggests that such protein(s) found in PHF-enriched fractions may derive from copurifying amyloid filaments rather than from PHF.     

Theoretical interstellar and prebiotic organic chemistry: A tentative methodology

A theoretical methodology for the systematic study of the interstellar molecules is proposed.Some examples, dealing with formaldehyde excited states, formyl radical and ion, reactivity of the excited states of formic acid, methyl cyanide and methyl acetylene, as well as the reaction path of formaldehyde photodecomposition are presented.Quantum chemical methods appear to be a powerful tool to study the structure and behaviour of molecules related with interstellar space and the Origin of Life.     

Role of interstellar molecules in prebiological evolution

Three generations of organic molecules in space are considered: interstellar molecules, molecules synthesised in protosolar cloud and molecules synthesised on the Earth. It is shown that there is no possibilities for amino acid polymers to be synthesised under interstellar cloud conditions. Molecules of the second generation were disintegrated during the Earth accumulation period. The problem of the origin of life is connected with the evolution of molecules of the third generation.     

INTERSTELLAR ICES STUDIED WITH THE INFRARED SPACE OBSERVATORY

The Infrared Space Observatory (ISO) was launched by the European Space Agency on 17 November 1995. The availability of spectra from the Short Wavelength Spectrometer (SWS) on ISO is a landmark in the study of interstellar ices and organics; they provide a wealth of data in the 2–20µ region of the spectrum covering the principal solid state resonances of condensed matter in interstellar clouds. We thus have the opportunity to study many species likely to be relevant to the inventory of CNO-bearing interstellar material present at the formation of our own and other planetary systems. This paper presents a brief overview of what has been learned from the data available so far. A comparison is made between the compositions of ices in molecular clouds, protostellar condensations and comets. Key areas of uncertainty are highlighted as a basis for future research.     

The Diffuse Interstellar Bands: A Tracer For Organics In The Diffuse Interstellar Medium?

The diffuse interstellar bands (DIBs) are absorption bands seen in the spectra of stars obscured by interstellar dust. DIBs are recognized as a tracer for free, organic molecules in the diffuse interstellar medium (ISM). The potential molecular carriers for the DIBs are discussed with an emphasis on neutral and ionized polycyclic aromatic hydrocarbons (PAHs) for which the most focused effort has been made to date. From the combined astronomical, laboratory and theoretical study, it is concluded that a distribution of free neutral and ionized complex organics (PAHs, fullerenes, unsaturated hydrocarbons) represents the most promising class of candidates to account for the DIBs. The case for aromatic hydrocarbons appears particularly strong. The implied widespread distribution of complex organics in the diffuse ISM bears profound implications for our understanding of the chemical complexity of the ISM, the evolution of prebiotic molecules and its impact on the origin and the evolution of life on early Earth through the exogenous delivery (cometary encounters and metoritic bombardments) of prebiotic organics.     

The chemical composition of interstellar molecular clouds

Relative abundances for molecules observed by radio astronomical techniques have been determined for several interstellar regions with differing physical properties.     

The chemical composition of interstellar molecular clouds

Relative abundances for molecules observed by radio astronomical techniques have been determined for several interstellar regions with differing physical properties.