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Life

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https://www.readbyqxmd.com/read/29329252/acknowledgement-to-reviewers-of-life-in-2017
#1
EDITORIAL
(no author information available yet)
Peer review is an essential part in the publication process, ensuring that Life maintains high quality standards for its published papers. In 2017, a total of 51 papers were published in the journal.[...].
January 12, 2018: Life
https://www.readbyqxmd.com/read/29301382/hydrogen-bonds-and-life-in-the-universe
#2
Giovanni Vladilo, Ali Hassanali
The scientific community is allocating more and more resources to space missions and astronomical observations dedicated to the search for life beyond Earth. This experimental endeavor needs to be backed by a theoretical framework aimed at defining universal criteria for the existence of life. With this aim in mind, we have explored which chemical and physical properties should be expected for life possibly different from the terrestrial one, but similarly sustained by genetic and catalytic molecules. We show that functional molecules performing genetic and catalytic tasks must feature a hierarchy of chemical interactions operating in distinct energy bands...
January 3, 2018: Life
https://www.readbyqxmd.com/read/29206171/kin-selection-in-the-rna-world
#3
Samuel R Levin, Stuart A West
Various steps in the RNA world required cooperation. Why did life's first inhabitants, from polymerases to synthetases, cooperate? We develop kin selection models of the RNA world to answer these questions. We develop a very simple model of RNA cooperation and then elaborate it to model three relevant issues in RNA biology: (1) whether cooperative RNAs receive the benefits of cooperation; (2) the scale of competition in RNA populations; and (3) explicit replicator diffusion and survival. We show: (1) that RNAs are likely to express partial cooperation; (2) that RNAs will need mechanisms for overcoming local competition; and (3) in a specific example of RNA cooperation, persistence after replication and offspring diffusion allow for cooperation to overcome competition...
December 5, 2017: Life
https://www.readbyqxmd.com/read/29207500/enrichment-of-circular-code-motifs-in-the-genes-of-the-yeast-saccharomyces-cerevisiae
#4
Christian J Michel, Viviane Nguefack Ngoune, Olivier Poch, Raymond Ripp, Julie D Thompson
A set X of 20 trinucleotides has been found to have the highest average occurrence in the reading frame, compared to the two shifted frames, of genes of bacteria, archaea, eukaryotes, plasmids and viruses. This set X has an interesting mathematical property, since X is a maximal C3 self-complementary trinucleotide circular code. Furthermore, any motif obtained from this circular code X has the capacity to retrieve, maintain and synchronize the original (reading) frame. Since 1996, the theory of circular codes in genes has mainly been developed by analysing the properties of the 20 trinucleotides of X, using combinatorics and statistical approaches...
December 3, 2017: Life
https://www.readbyqxmd.com/read/29189763/formation-and-stability-of-prebiotically-relevant-vesicular-systems-in-terrestrial-geothermal-environments
#5
Manesh Prakash Joshi, Anupam Samanta, Gyana Ranjan Tripathy, Sudha Rajamani
Terrestrial geothermal fields and oceanic hydrothermal vents are considered as candidate environments for the emergence of life on Earth. Nevertheless, the ionic strength and salinity of oceans present serious limitations for the self-assembly of amphiphiles, a process that is fundamental for the formation of first protocells. Consequently, we systematically characterized the efficiency of amphiphile assembly, and vesicular stability, in terrestrial geothermal environments, both, under simulated laboratory conditions and in hot spring water samples (collected from Ladakh, India, an Astrobiologically relevant site)...
November 30, 2017: Life
https://www.readbyqxmd.com/read/29189724/effects-of-trimetaphosphate-on-abiotic-formation-and-hydrolysis-of-peptides
#6
Izabela K Sibilska, Bingming Chen, Lingjun Li, John Yin
The primordial Earth probably had most of the factors needed for the emergence and development of life. It is believed that it had not only water, but also simple inorganic and organic materials. While studies since the 1950s on the origins of organic matter have established key roles for amino acids, conditions that would have promoted their condensation to make polymers, such as peptides or proteins, have yet to be fully defined. The condensation of amino acids in a water-rich environment is not thermodynamically favored...
November 30, 2017: Life
https://www.readbyqxmd.com/read/29186049/what-does-the-rna-world-mean-to-the-origin-of-life
#7
Wentao Ma
Corresponding to life's two distinct aspects: Darwinian evolution and self-sustainment, the origin of life should also split into two issues: the origin of Darwinian evolution and the arising of self-sustainment. Because the "self-sustainment" we concern about life should be the self-sustainment of a relevant system that is "defined" by its genetic information, the self-sustainment could not have arisen before the origin of Darwinian evolution, which was just marked by the emergence of genetic information. The logic behind the idea of the RNA world is not as tenable as it has been believed...
November 29, 2017: Life
https://www.readbyqxmd.com/read/29186916/ecology-and-evolution-in-the-rna-world-dynamics-and-stability-of-prebiotic-replicator-systems
#8
REVIEW
András Szilágyi, István Zachar, István Scheuring, Ádám Kun, Balázs Könnyű, Tamás Czárán
As of today, the most credible scientific paradigm pertaining to the origin of life on Earth is undoubtedly the RNA World scenario. It is built on the assumption that catalytically active replicators (most probably RNA-like macromolecules) may have been responsible for booting up life almost four billion years ago. The many different incarnations of nucleotide sequence (string) replicator models proposed recently are all attempts to explain on this basis how the genetic information transfer and the functional diversity of prebiotic replicator systems may have emerged, persisted and evolved into the first living cell...
November 27, 2017: Life
https://www.readbyqxmd.com/read/29165335/integral-phylogenomic-approach-over-ilex-l-species-from-southern-south-america
#9
Jimena Cascales, Mariana Bracco, Mariana J Garberoglio, Lidia Poggio, Alexandra M Gottlieb
The use of molecular markers with inadequate variation levels has resulted in poorly resolved phylogenetic relationships within Ilex. Focusing on southern South American and Asian species, we aimed at contributing informative plastid markers. Also, we intended to gain insights into the nature of morphological and physiological characters used to identify species. We obtained the chloroplast genomes of I.paraguariensis and I. dumosa, and combined these with all the congeneric plastomes currently available to accomplish interspecific comparisons and multilocus analyses...
November 22, 2017: Life
https://www.readbyqxmd.com/read/29160840/cloning-and-molecular-characterization-of-an-alpha-glucosidase-malh-from-the-halophilic-archaeon-haloquadratum-walsbyi
#10
Mara F Cuebas-Irizarry, Ricardo A Irizarry-Caro, Carol López-Morales, Keyla M Badillo-Rivera, Carlos M Rodríguez-Minguela, Rafael Montalvo-Rodríguez
We report the heterologous expression and molecular characterization of the first extremely halophilic alpha-glucosidase (EC 3.2.1.20) from the archaeon Haloquadratum walsbyi. A 2349 bp region (Hqrw_2071) from the Hqr. walsbyi C23 annotated genome was PCR-amplified and the resulting amplicon ligated into plasmid pET28b(+), expressed in E. coli Rosetta cells, and the resulting protein purified by Ni-NTA affinity chromatography. The recombinant protein showed an estimated molecular mass of 87 kDa, consistent with the expected value of the annotated protein, and an optimal activity for the hydrolysis of α-PNPG was detected at 40 °C, and at pH 6...
November 21, 2017: Life
https://www.readbyqxmd.com/read/29156594/chemical-transformations-in-proto-cytoplasmic-media-phosphorus-coupling-in-the-silica-hydrogel-phase
#11
Ian B Gorrell, Timothy W Henderson, Kamal Albdeery, Philip M Savage, Terence P Kee
It has been proposed that prebiotic chemical studies on the emergence of primitive life would be most relevant when performed in a hydrogel, rather than an aqueous, environment. In this paper we describe the ambient temperature coupling of phosphorus oxyacids [Pi] mediated by Fe(II) under aerobic conditions within a silica hydrogel (SHG) environment. We have chosen to examine SHGs as they have considerable geological precedence as key phases in silicification en route to rock formation. Following a description of the preparation and characterization studies on our SHG formulations, coupling experiments between Pi species are described across multiple permutations of (i) Pi compound; (ii) gel formulation; (iii) metal salt additive; and (iv) pH-modifying agent...
November 19, 2017: Life
https://www.readbyqxmd.com/read/29135960/the-impact-of-salts-on-single-chain-amphiphile-membranes-and-implications-for-the-location-of-the-origin-of-life
#12
REVIEW
Sarah Maurer
One of the key steps in the origins of life was the formation of a membrane to separate protocells from their environment. These membranes are proposed to have been formed out of single chain amphiphiles, which are less stable than the dialkyl lipids used to form modern membranes. This lack of stability, specifically for decanoate, is often used to refute ocean locations for the origins of life. This review addresses the formation of membranes in hydrothermal-vent like conditions, as well as other environmental constraints...
November 14, 2017: Life
https://www.readbyqxmd.com/read/29099079/evolutionary-conflict-leads-to-innovation-symmetry-breaking-in-a-spatial-model-of-rna-like-replicators
#13
Samuel H A von der Dunk, Enrico Sandro Colizzi, Paulien Hogeweg
Molecules that replicate in trans are vulnerable to evolutionary extinction because they decrease the catalysis of replication to become more available as a template for replication. This problem can be alleviated with higher-level selection that clusters molecules of the same phenotype, favouring those groups that contain more catalysis. Here, we study a simple replicator model with implicit higher-level selection through space. We ask whether the functionality of such system can be enhanced when molecules reproduce through complementary replication, representing RNA-like replicators...
November 2, 2017: Life
https://www.readbyqxmd.com/read/29088116/the-role-of-templating-in-the-emergence-of-rna-from-the-prebiotic-chemical-mixture
#14
Andrew S Tupper, Kevin Shi, Paul G Higgs
Biological RNA is a uniform polymer in three senses: it uses nucleotides of a single chirality; it uses only ribose sugars and four nucleobases rather than a mixture of other sugars and bases; and it uses only 3'-5' bonds rather than a mixture of different bond types. We suppose that prebiotic chemistry would generate a diverse mixture of potential monomers, and that random polymerization would generate non-uniform strands of mixed chirality, monomer composition, and bond type. We ask what factors lead to the emergence of RNA from this mixture...
October 31, 2017: Life
https://www.readbyqxmd.com/read/29088079/smore-synteny-modulator-of-repetitive-elements
#15
Sarah J Berkemer, Anne Hoffmann, Cameron R A Murray, Peter F Stadler
Several families of multicopy genes, such as transfer ribonucleic acids (tRNAs) and ribosomal RNAs (rRNAs), are subject to concerted evolution, an effect that keeps sequences of paralogous genes effectively identical. Under these circumstances, it is impossible to distinguish orthologs from paralogs on the basis of sequence similarity alone. Synteny, the preservation of relative genomic locations, however, also remains informative for the disambiguation of evolutionary relationships in this situation. In this contribution, we describe an automatic pipeline for the evolutionary analysis of such cases that use genome-wide alignments as a starting point to assign orthology relationships determined by synteny...
October 31, 2017: Life
https://www.readbyqxmd.com/read/29072614/a-statistical-approach-to-illustrate-the-challenge-of-astrobiology-for-public-outreach
#16
Frédéric Foucher, Keyron Hickman-Lewis, Frances Westall, André Brack
In this study, we attempt to illustrate the competition that constitutes the main challenge of astrobiology, namely the competition between the probability of extraterrestrial life and its detectability. To illustrate this fact, we propose a simple statistical approach based on our knowledge of the Universe and the Milky Way, the Solar System, and the evolution of life on Earth permitting us to obtain the order of magnitude of the distance between Earth and bodies inhabited by more or less evolved past or present life forms, and the consequences of this probability for the detection of associated biosignatures...
October 26, 2017: Life
https://www.readbyqxmd.com/read/29035326/prebiotic-rna-network-formation-a-taxonomy-of-molecular-cooperation
#17
Cole Mathis, Sanjay N Ramprasad, Sara Imari Walker, Niles Lehman
Cooperation is essential for evolution of biological complexity. Recent work has shown game theoretic arguments, commonly used to model biological cooperation, can also illuminate the dynamics of chemical systems. Here we investigate the types of cooperation possible in a real RNA system based on the Azoarcus ribozyme, by constructing a taxonomy of possible cooperative groups. We construct a computational model of this system to investigate the features of the real system promoting cooperation. We find triplet interactions among genotypes are intrinsically biased towards cooperation due to the particular distribution of catalytic rate constants measured empirically in the real system...
October 16, 2017: Life
https://www.readbyqxmd.com/read/28974048/hydrothermal-microflow-technology-as-a-research-tool-for-origin-of-life-studies-in-extreme-earth-environments
#18
REVIEW
Kunio Kawamura
Although studies about the origin of life are a frontier in science and a number of effective approaches have been developed, drawbacks still exist. Examples include: (1) simulation of chemical evolution experiments (which were demonstrated for the first time by Stanley Miller); (2) approaches tracing back the most primitive life-like systems (on the basis of investigations of present organisms); and (3) constructive approaches for making life-like systems (on the basis of molecular biology), such as in vitro construction of the RNA world...
October 2, 2017: Life
https://www.readbyqxmd.com/read/28914790/ancient-living-organisms-escaping-from-or-imprisoned-in-the-vents
#19
REVIEW
J Baz Jackson
We have recently criticised the natural pH gradient hypothesis which purports to explain how the difference in pH between fluid issuing from ancient alkali vents and the more acidic Hadean ocean could have driven molecular machines that catalyse reactions that are useful in prebiotic and autotrophic chemistry. In this article, we temporarily suspend our earlier criticism while we consider difficulties for primitive organisms to have managed their energy supply and to have left the vents and become free-living...
September 15, 2017: Life
https://www.readbyqxmd.com/read/29061955/double-hydrogen-bonding-between-side-chain-carboxyl-groups-in-aqueous-solutions-of-poly-%C3%AE-l-malic-acid-implication-for-the-evolutionary-origin-of-nucleic-acids
#20
Brian R Francis, Kevin Watkins, Jan Kubelka
The RNA world hypothesis holds that in the evolutionary events that led to the emergence of life RNA preceded proteins and DNA and is supported by the ability of RNA to act as both a genetic polymer and a catalyst. On the other hand, biosynthesis of nucleic acids requires a large number of enzymes and chemical synthesis of RNA under presumed prebiotic conditions is complicated and requires many sequential steps. These observations suggest that biosynthesis of RNA is the end product of a long evolutionary process...
August 28, 2017: Life
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