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Origins of Life and Evolution of the Biosphere

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https://www.readbyqxmd.com/read/29127550/a-proposal-of-the-ur-proteome
#1
Miryam Palacios-Pérez, Fernando Andrade-Díaz, Marco V José
Herein we outline a plausible proteome, encoded by assuming a primeval RNY genetic code. We unveil the primeval phenotype by using only the RNA genotype; it means that we recovered the most ancestral proteome, mostly made of the 8 amino acids encoded by RNY triplets. By looking at those fragments, it is noticeable that they are positioned, not at catalytic sites, but in the cofactor binding sites. It implies that the stabilization of a molecule appeared long before its catalytic activity, and therefore the Ur-proteome comprised a set of proteins modules that corresponded to Cofactor Stabilizing Binding Sites (CSBSs), which we call the primitive bindome...
November 10, 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/29119380/chiral-symmetry-breaking-in-peptide-systems-during-formation-of-life-on-earth
#2
Konstantin K Konstantinov, Alisa F Konstantinova
Chiral symmetry breaking in complex chemical systems with a large number of amino acids and a large number of similar reactions was considered. It was shown that effective averaging over similar reaction channels may result in very weak effective enantioselectivity of forward reactions, which does not allow most of the known models to result in chiral symmetry breaking during formation of life on Earth. Models with simple and catalytic synthesis of a single amino acid, formation of peptides up to length five, and sedimentation of insoluble pair of substances were considered...
November 8, 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/29082465/phenotypic-graphs-and-evolution-unfold-the-standard-genetic-code-as-the-optimal
#3
Gabriel S Zamudio, Marco V José
In this work, we explicitly consider the evolution of the Standard Genetic Code (SGC) by assuming two evolutionary stages, to wit, the primeval RNY code and two intermediate codes in between. We used network theory and graph theory to measure the connectivity of each phenotypic graph. The connectivity values are compared to the values of the codes under different randomization scenarios. An error-correcting optimal code is one in which the algebraic connectivity is minimized. We show that the SGC is optimal in regard to its robustness and error-tolerance when compared to all random codes under different assumptions...
October 29, 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28875241/primary-formation-path-of-formaldehyde-in-hydrothermal-vents
#4
Satoshi Inaba
Formaldehyde is abundant in the universe and one of the fundamental molecules for life. Hydrothermal vents produce a substantial amount of hydrogen molecules by serpentinization and promote reductive reactions of single carbon compounds. The abundance of formaldehyde is expected to be low due to the high Gibbs free energy in hydrothermal vents. We consider two competing formation pathways of formaldehyde: (1) the reduction of CO by H2 and (2) the reduction of HCOOH by H2 to form a methanediol, followed by the dehydration of the methanediol...
September 5, 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28791552/mechanism-for-the-coupled-photochemistry-of-ammonia-and-acetylene-implications-for-giant-planets-comets-and-interstellar-organic-synthesis
#5
Thomas C Keane
Laboratory studies provide a fundamental understanding of photochemical processes in planetary atmospheres. Photochemical reactions taking place on giant planets like Jupiter and possibly comets and the interstellar medium are the subject of this research. Reaction pathways are proposed for the coupled photochemistry of NH3 (ammonia) and C2H2 (acetylene) within the context Jupiter's atmosphere. We then extend the discussion to the Great Red Spot, Extra-Solar Giant Planets, Comets and Interstellar Organic Synthesis...
September 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28744686/polycondensation-of-asparagine-comprising-dipeptides-in-aqueous-media-a-simulation-of-polypeptide-formation-in-primordial-earth-hydrosphere
#6
Toratane Munegumi, Naoya Tanikawa
Asparagine and aspartic acid might have mutually transformed in the primordial hydrosphere of the earth, if ammonia and aspartic acid had existed in equilibrium. These amino acids seem to contribute to polypeptides, while the simple amino acids glycine and alanine easily form cyclic dipeptides and do not achieve long peptide chains. Asparagine-comprising dipeptides contribute some kinds of activation forms of dipeptides because these can polymerize faster than asparagine only. The new finding of polypeptide formation suggests a pathway of sequential polypeptides to evolve a diversity of polypeptides...
September 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28470374/cataclysm-no-more-new-views-on-the-timing-and-delivery-of-lunar-impactors
#7
Nicolle E B Zellner
If properly interpreted, the impact record of the Moon, Earth's nearest neighbour, can be used to gain insights into how the Earth has been influenced by impacting events since its formation ~4.5 billion years (Ga) ago. However, the nature and timing of the lunar impactors - and indeed the lunar impact record itself - are not well understood. Of particular interest are the ages of lunar impact basins and what they tell us about the proposed "lunar cataclysm" and/or the late heavy bombardment (LHB), and how this impact episode may have affected early life on Earth or other planets...
September 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28432500/walking-over-4-gya-chemical-evolution-from-photochemistry-to-mineral-and-organic-chemistries-leading-to-an-rna-world
#8
REVIEW
Kunio Kawamura, Marie-Christine Maurel
Here we overview the chemical evolution of RNA molecules from inorganic material through mineral-mediated RNA formation compatible with the plausible early Earth environments. Pathways from the gas-phase reaction to the formation of nucleotides, activation and oligomerization of nucleotides, seem to be compatible with specific environments. However, how these steps interacted is not clear since the chemical conditions are frequently different and can be incompatible between them; thus the products would have migrated from one place to another, suitable for further chemical evolution...
September 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28361302/transfer-of-asymmetry-between-proteinogenic-amino-acids-under-harsh-conditions
#9
Arkadii V Tarasevych, Thomas Vives, Valeriy N Snytnikov, Jean-Claude Guillemin
The heating above 400 °C of serine, cysteine, selenocysteine and threonine leads to a complete decomposition of the amino acids and to the formation in low yields of alanine for the three formers and of 2-aminobutyric acid for the latter. At higher temperature, this amino acid is observed only when sublimable α-alkyl-α-amino acids are present, and with an enantiomeric excess dependent on several parameters. Enantiopure or enantioenriched Ser, Cys, Sel or Thr is not able to transmit its enantiomeric excess to the amino acid formed during its decomposition...
September 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28210992/the-comparison-of-hydrochloric-acid-and-phosphoric%C3%A2-acid-treatments-in-the-preparation-of-montmorillonite-catalysts-for-rna-synthesis
#10
Michael Frank Aldersley, Prakash C Joshi, Yixing Huang
The treatment of clay minerals with a preliminary acid wash and titration to pH 7 has proven to generate catalysts for the most interesting of oligomerization reactions in which activated RNA-nucleotides generate oligomers up to 40-mers. Significantly, not all clay minerals become catalytic following this treatment and none are catalytic in the absence of such treatment. The washing procedure has been modified and explored further using phosphoric acid and the outcomes are compared to those obtained when clay samples are prepared following a hydrochloric acid wash...
September 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28160163/nucleotide-selectivity-in-abiotic-rna-polymerization-reactions
#11
Kristin M Coari, Rebecca C Martin, Kopal Jain, Linda B McGown
In order to establish an RNA world on early Earth, the nucleotides must form polymers through chemical rather than biochemical reactions. The polymerization products must be long enough to perform catalytic functions, including self-replication, and to preserve genetic information. These functions depend not only on the length of the polymers, but also on their sequences. To date, studies of abiotic RNA polymerization generally have focused on routes to polymerization of a single nucleotide and lengths of the homopolymer products...
September 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28078499/carbonaceous-chondrite-meteorites-the-chronicle-of-a-potential-evolutionary-path-between-stars-and-life
#12
Sandra Pizzarello, Everett Shock
The biogenic elements, H, C, N, O, P and S, have a long cosmic history, whose evolution can still be observed in diverse locales of the known universe, from interstellar clouds of gas and dust, to pre-stellar cores, nebulas, protoplanetary discs, planets and planetesimals. The best analytical window into this cosmochemical evolution as it neared Earth has been provided so far by the small bodies of the Solar System, some of which were not significantly altered by the high gravitational pressures and temperatures that accompanied the formation of larger planets and may carry a pristine record of early nebular chemistry...
September 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28025749/farewell-to-a-friend
#13
André Brack
No abstract text is available yet for this article.
September 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/27783188/interaction-at-ambient-temperature-and-80%C3%A2-%C3%A2-c-between-minerals-and-artificial-seawaters-resembling-the-present-ocean-composition-and-that-of-4-0-billion-years-ago
#14
Cristine E A Carneiro, Antonio C Stabile, Frederico P Gomes, Antonio C S da Costa, Cássia T B V Zaia, Dimas A M Zaia
Probably one of the most important roles played by minerals in the origin of life on Earth was to pre-concentrate biomolecules from the prebiotic seas. There are other ways to pre concentrate biomolecules such as wetting/drying cycles and freezing/sublimation. However, adsorption is most important. If the pre-concentration did not occur-because of degradation of the minerals-other roles played by them such as protection against degradation, formation of polymers, or even as primitive cell walls would be seriously compromised...
September 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/27771860/can-an-imidazole-be-formed-from-an-alanyl-seryl-glycine-tripeptide-under-possible-prebiotic-conditions
#15
Alberto Vázquez-Salazar, George Tan, Amanda Stockton, Renato Fani, Arturo Becerra, Antonio Lazcano
The five-membered heterocyclic imidazole group, which is an essential component of purines, histidine and many cofactors, has been abiotically synthesized in different model experiments that attempt to simulate the prebiotic environment. The evolutionary significance of imidazoles is highlighted not only by its presence in nucleic acid components and in histidine, but also by experimental reports of its ability to restore the catalytic activity of ribozymes. However, as of today there are no reports of histidine in carbonaceous chondrites, and although the abiotic synthesis of His reported by Shen et al...
September 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28815473/publication-of-abstracts-and-full-papers-from-the-international-conference-on-the-origin-of-life-san-diego-2017
#16
EDITORIAL
Alan W Schwartz
No abstract text is available yet for this article.
August 16, 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28812194/amorphous-silica-promoted-lysine-dimerization-a-thermodynamic-prediction
#17
Norio Kitadai, Kumiko Nishiuchi, Akari Nishii, Keisuke Fukushi
It has long been suggested that mineral surfaces played a crucial role in the abiotic polymerization of amino acids that preceded the origin of life. Nevertheless, it remains unclear where the prebiotic process took place on the primitive Earth, because the amino acid-mineral interaction and its dependence on environmental conditions have yet to be understood adequately. Here we examined experimentally the adsorption of L-lysine (Lys) and its dimer (LysLys) on amorphous silica over a wide range of pH, ionic strength, adsorbate concentration, and the solid/water ratio, and determined the reaction stoichiometries and the equilibrium constants based on the extended triple-layer model (ETLM)...
August 15, 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28702783/origins-of-life-research-a-bibliometric-approach
#18
Arsev Umur Aydinoglu, Zehra Taşkın
This study explores the collaborative nature and interdisciplinarity of the origin(s) of life (OoL) research community. Although OoL research is one of the oldest topics in philosophy, religion, and science; to date there has been no review of the field utilizing bibliometric measures. A dataset of 5647 publications that are tagged as OoL, astrobiology, exobiology, and prebiotic chemistry is analyzed. The most prolific authors (Raulin, Ehrenfreund, McKay, Cleaves, Cockell, Lazcano, etc.), most cited scholars and their articles (Miller 1953, Gilbert 1986, Chyba & Sagan 1992, Wȁchtershȁuser 1988, etc...
July 13, 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28689315/enantiomer-selective-photo-induced-reaction-of-protonated-tryptophan-with-disaccharides-in-the-gas-phase
#19
Thuc N Doan, Akimasa Fujihara
In order to investigate chemical evolution in interstellar molecular clouds, enantiomer-selective photo-induced chemical reactions between an amino acid and disaccharides in the gas phase were examined using a tandem mass spectrometer containing an electrospray ionization source and a cold ion trap. Ultraviolet photodissociation mass spectra of cold gas-phase noncovalent complexes of protonated tryptophan (Trp) enantiomers with disaccharides consisting of two D-glucose units, such as D-maltose or D-cellobiose, were obtained by photoexcitation of the indole ring of Trp...
July 8, 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28685374/environmental-adaptation-from-the-origin-of-life-to-the-last-universal-common-ancestor
#20
Marjorie D Cantine, Gregory P Fournier
Extensive fundamental molecular and biological evolution took place between the prebiotic origins of life and the state of the Last Universal Common Ancestor (LUCA). Considering the evolutionary innovations between these two endpoints from the perspective of environmental adaptation, we explore the hypothesis that LUCA was temporally, spatially, and environmentally distinct from life's earliest origins in an RNA world. Using this lens, we interpret several molecular biological features as indicating an environmental transition between a cold, radiation-shielded origin of life and a mesophilic, surface-dwelling LUCA...
July 6, 2017: Origins of Life and Evolution of the Biosphere
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