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Origins of Life and Evolution of the Biosphere

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https://www.readbyqxmd.com/read/29713988/in-the-beginning-was-a-mutualism-on-the-origin-of-translation
#1
Marko Vitas, Andrej Dobovišek
The origin of translation is critical for understanding the evolution of life, including the origins of life. The canonical genetic code is one of the most dominant aspects of life on this planet, while the origin of heredity is one of the key evolutionary transitions in living world. Why the translation apparatus evolved is one of the enduring mysteries of molecular biology. Assuming the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems which only subsequently acquired the capacity of genetic heredity, we propose and discuss possible mechanisms, basic aspects of the emergence and subsequent molecular evolution of translation and ribosomes, as well as enzymes as we know them today...
April 30, 2018: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/29705890/selective-formation-of-ser-his-dipeptide-via-phosphorus-activation
#2
Wanyun Shu, Yongfei Yu, Su Chen, Xia Yan, Yan Liu, Yufen Zhao
The Ser-His dipeptide is the shortest active peptide. This dipeptide not only hydrolyzes proteins and DNA but also catalyzes the formation of peptides and phosphodiester bonds. As a potential candidate for the prototype of modern hydrolase, Ser-His has attracted increasing attention. To explore if Ser-His could be obtained efficiently in the prebiotic condition, we investigated the reactions of N-DIPP-Ser with His or other amino acids in an aqueous system. We observed that N-DIPP-Ser incubated with His can form Ser-His more efficiently than with other amino acids...
April 29, 2018: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/29502283/acetyl-phosphate-as-a-primordial-energy-currency-at-the-origin-of-life
#3
Alexandra Whicher, Eloi Camprubi, Silvana Pinna, Barry Herschy, Nick Lane
Metabolism is primed through the formation of thioesters via acetyl CoA and the phosphorylation of substrates by ATP. Prebiotic equivalents such as methyl thioacetate and acetyl phosphate have been proposed to catalyse analogous reactions at the origin of life, but their propensity to hydrolyse challenges this view. Here we show that acetyl phosphate (AcP) can be synthesised in water within minutes from thioacetate (but not methyl thioacetate) under ambient conditions. AcP is stable over hours, depending on temperature, pH and cation content, giving it an ideal poise between stability and reactivity...
March 3, 2018: 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
#4
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...
March 2018: 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
#5
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...
March 2018: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28875241/primary-formation-path-of-formaldehyde-in-hydrothermal-vents
#6
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...
March 2018: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28812194/amorphous-silica-promoted-lysine-dimerization-a-thermodynamic-prediction
#7
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)...
March 2018: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28702783/origins-of-life-research-a-bibliometric-approach
#8
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...
March 2018: 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
#9
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...
March 2018: 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
#10
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...
March 2018: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28660466/identity-elements-of-trna-as-derived-from-information-analysis
#11
Gabriel S Zamudio, Marco V José
The decipherment of the tRNA's operational code, known as the identity problem, requires the location of the sites in the tRNA structure that are involved in their correct recognition by the corresponding aminoacyl-tRNA synthetase. In this work, we determine the identity elements of each tRNA isoacceptor by means of the variation of information measure from information theory. We show that all isoacceptors exhibit sites associated with some bases of the anticodon. These sites form clusters that are scattered along the tRNA structure...
March 2018: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28593333/survival-and-adaptation-of-the-thermophilic-species-geobacillus-thermantarcticus-in-simulated-spatial-conditions
#12
Paola Di Donato, Ida Romano, Vincenza Mastascusa, Annarita Poli, Pierangelo Orlando, Mariagabriella Pugliese, Barbara Nicolaus
Astrobiology studies the origin and evolution of life on Earth and in the universe. According to the panspermia theory, life on Earth could have emerged from bacterial species transported by meteorites, that were able to adapt and proliferate on our planet. Therefore, the study of extremophiles, i.e. bacterial species able to live in extreme terrestrial environments, can be relevant to Astrobiology studies. In this work we described the ability of the thermophilic species Geobacillus thermantarcticus to survive after exposition to simulated spatial conditions including temperature's variation, desiccation, X-rays and UVC irradiation...
March 2018: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28484901/racemization-of-valine-by-impact-induced-heating
#13
Yoshihiro Furukawa, Atsushi Takase, Toshimori Sekine, Takeshi Kakegawa, Takamichi Kobayashi
Homochirality plays an important role in all living organisms but its origin remains unclear. It also remains unclear whether such chiral molecules survived terrestrial heavy impact events. Impacts of extraterrestrial objects on early oceans were frequent and could have affected the chirality of oceanic amino acids when such amino acids accumulated during impacts. This study investigated the effects of shock-induced heating on enantiomeric change of valine with minerals such as olivine ([Mg0.9 , Fe0.1 ]2 SiO4 ), hematite (Fe2 O3 ), and calcite (CaCO3 )...
March 2018: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/29392543/salinity-effects-on-the-adsorption-of-nucleic-acid-compounds-on-na-montmorillonite-a-prebiotic-chemistry-experiment
#14
Saúl A Villafañe-Barajas, João Paulo T Baú, María Colín-García, Alicia Negrón-Mendoza, Alejandro Heredia-Barbero, Teresa Pi-Puig, Dimas A M Zaia
Any proposed model of Earth's primitive environments requires a combination of geochemical variables. Many experiments are prepared in aqueous solutions and in the presence of minerals. However, most sorption experiments are performed in distilled water, and just a few in seawater analogues, mostly inconsistent with a representative primitive ocean model. Therefore, it is necessary to perform experiments that consider the composition and concentration of dissolved salts in the early ocean to understand how these variables could have affected the absorption of organic molecules into minerals...
February 1, 2018: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28474281/on-the-ability-of-formaldehyde-to-act-as-a-tethering-catalyst-in-water
#15
Mohammad P Jamshidi, Melissa J MacDonald, André M Beauchemin
The low concentration issue is a fundamental challenge when it comes to prebiotic chemistry, as macromolecular systems need to be assembled via intermolecular reactions, and this is inherently difficult in dilute solutions. This is especially true when the reactions are challenging, and reactions that proceeded more rapidly could have dictated chemical evolution. Herein we establish that formaldehyde is capable of catalyzing, via temporary intramolecularity, a challenging reaction in water at low concentrations, thus providing an alternative to other approaches that can either lead to higher concentrations or higher effective molarities...
December 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28361301/anoxic-and-oxic-oxidation-of-rocks-containing-fe-ii-mg-silicates-and-fe-ii-monosulfides-as-source-of-fe-iii-minerals-and-hydrogen-geobiotropy
#16
Marie-Paule Bassez
In this article, anoxic and oxic hydrolyses of rocks containing Fe (II) Mg-silicates and Fe (II)-monosulfides are analyzed at 25 °C and 250-350 °C. A table of the products is drawn. It is shown that magnetite and hydrogen can be produced during low-temperature (25 °C) anoxic hydrolysis/oxidation of ferrous silicates and during high-temperature (250 °C) anoxic hydrolysis/oxidation of ferrous monosulfides. The high-T (350 °C) anoxic hydrolysis of ferrous silicates leads mainly to ferric oxides/hydroxides such as the hydroxide ferric trihydroxide, the oxide hydroxide goethite/lepidocrocite and the oxide hematite, and to Fe(III)-phyllosilicates...
December 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/27933421/erratum-to-an-experimental-framework-for-generating-evolvable-chemical-systems-in-the-laboratory
#17
David A Baum, Kalin Vetsigian
No abstract text is available yet for this article.
December 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/27896547/chemical-analysis-of-a-miller-type-complex-prebiotic-broth-part-ii-gas-oil-water-and-the-oil-water-interface
#18
Sabrina Scherer, Eva Wollrab, Luca Codutti, Teresa Carlomagno, Stefan Gomes da Costa, Andreas Volkmer, Amela Bronja, Oliver J Schmitz, Albrecht Ott
We have analyzed the chemical variety obtained by Miller-Urey-type experiments using nuclear magnetic resonance (NMR) spectroscopy and coherent anti-Stokes Raman scattering (CARS) spectroscopy, gas chromatography followed by mass spectrometry (GC/MS) and two-dimensional gas chromatography followed by mass spectrometry (GCxGC/MS). In the course of a running Miller-Urey-type experiment, a hydrophobic organic layer emerged besides the hydrophilic aqueous phase and the gaseous phase that were initially present...
December 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/27864699/an-experimental-framework-for-generating-evolvable-chemical-systems-in-the-laboratory
#19
David A Baum, Kalin Vetsigian
Most experimental work on the origin of life has focused on either characterizing the chemical synthesis of particular biochemicals and their precursors or on designing simple chemical systems that manifest life-like properties such as self-propagation or adaptive evolution. Here we propose a new class of experiments, analogous to artificial ecosystem selection, where we select for spontaneously forming self-propagating chemical assemblages in the lab and then seek evidence of a response to that selection as a key indicator that life-like chemical systems have arisen...
December 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/27807660/encapsulation-of-nucleic-acids-into-giant-unilamellar-vesicles-by-freeze-thaw-a-way-protocells-may-form
#20
Hai Qiao, Na Hu, Jin Bai, Lili Ren, Qing Liu, Liaoqiong Fang, Zhibiao Wang
Protocells are believed to consist of a lipid membrane and encapsulated nucleic acid. As the lipid membrane is impermeable to macromolecules like nucleic acids, the processes by which nucleic acids become encapsulated inside lipid membrane compartments are still unknown. In this paper, a freeze-thaw method was modified and applied to giant unilamellar vesicles (GUVs) and deoxyribonucleic acid (DNA) in mixed solution resulting in the efficient encapsulation of 6.4 kb plasmid DNA and similar length linear DNA into GUVs...
December 2017: Origins of Life and Evolution of the Biosphere
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