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Life, Volume 3, Issue 3 (September 2013), Pages 363-517

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Editorial

Jump to: Research, Review

Open AccessEditorial Extremophiles and Extreme Environments
Life 2013, 3(3), 482-485; doi:10.3390/life3030482
Received: 2 August 2013 / Accepted: 5 August 2013 / Published: 7 August 2013
Cited by 1 | PDF Full-text (315 KB) | HTML Full-text | XML Full-text
Abstract
Over the last decades, the study of extremophiles has providing ground breaking discoveries that challenge the paradigms of modern biology and make us rethink intriguing questions such as "what is life?", "what are the limits of life?", and "what are the fundamental [...] Read more.
Over the last decades, the study of extremophiles has providing ground breaking discoveries that challenge the paradigms of modern biology and make us rethink intriguing questions such as "what is life?", "what are the limits of life?", and "what are the fundamental features of life?". These findings and possibilities have made the study of life in extreme environments one of the most exciting areas of research in recent decades. However, despite the latest advances we are just in the beginning of exploring and characterizing the world of extremophiles. This special issue discusses several aspects of these fascinating organisms, exploring their habitats, biodiversity, ecology, evolution, genetics, biochemistry, and biotechnological applications in a collection of exciting reviews and original articles written by leading experts and research groups in the field. [...] Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)

Research

Jump to: Editorial, Review

Open AccessArticle Phosphate Activation via Reduced Oxidation State Phosphorus (P). Mild Routes to Condensed-P Energy Currency Molecules
Life 2013, 3(3), 386-402; doi:10.3390/life3030386
Received: 14 May 2013 / Revised: 8 June 2013 / Accepted: 13 June 2013 / Published: 19 July 2013
Cited by 4 | PDF Full-text (906 KB) | HTML Full-text | XML Full-text
Abstract
The emergence of mechanisms for phosphorylating organic and inorganic molecules is a key step en route to the earliest living systems. At the heart of all contemporary biochemical systems reside reactive phosphorus (P) molecules (such as adenosine triphosphate, ATP) as energy currency [...] Read more.
The emergence of mechanisms for phosphorylating organic and inorganic molecules is a key step en route to the earliest living systems. At the heart of all contemporary biochemical systems reside reactive phosphorus (P) molecules (such as adenosine triphosphate, ATP) as energy currency molecules to drive endergonic metabolic processes and it has been proposed that a predecessor of such molecules could have been pyrophosphate [P2O74−; PPi(V)]. Arguably the most geologically plausible route to PPi(V) is dehydration of orthophosphate, Pi(V), normally a highly endergonic process in the absence of mechanisms for activating Pi(V). One possible solution to this problem recognizes the presence of reactive-P containing mineral phases, such as schreibersite [(Fe,Ni)3P] within meteorites whose abundance on the early Earth would likely have been significant during a putative Hadean-Archean heavy bombardment. Here, we propose that the reduced oxidation state P-oxyacid, H-phosphite [HPO32−; Pi(III)] could have activated Pi(V) towards condensation via the intermediacy of the condensed oxyacid pyrophosphite [H2P2O52−; PPi(III)]. We provide geologically plausible provenance for PPi(III) along with evidence of its ability to activate Pi(V) towards PPi(V) formation under mild conditions (80 °C) in water. Full article
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Open AccessArticle A Necessary Condition for Coexistence of Autocatalytic Replicators in a Prebiotic Environment
Life 2013, 3(3), 403-420; doi:10.3390/life3030403
Received: 22 April 2013 / Revised: 13 June 2013 / Accepted: 17 June 2013 / Published: 24 July 2013
Cited by 1 | PDF Full-text (642 KB) | HTML Full-text | XML Full-text
Abstract
A necessary, but not sufficient, mathematical condition for the coexistence of short replicating species is presented here. The mathematical condition is obtained for a prebiotic environment, simulated as a fed-batch reactor, which combines monomer recycling, variable reaction order and a fixed monomer [...] Read more.
A necessary, but not sufficient, mathematical condition for the coexistence of short replicating species is presented here. The mathematical condition is obtained for a prebiotic environment, simulated as a fed-batch reactor, which combines monomer recycling, variable reaction order and a fixed monomer inlet flow with two replicator types and two monomer types. An extensive exploration of the parameter space in the model validates the robustness and efficiency of the mathematical condition, with nearly 1.7% of parameter sets meeting the condition and half of those exhibiting sustained coexistence. The results show that it is possible to generate a condition of coexistence, where two replicators sustain a linear growth simultaneously for a wide variety of chemistries, under an appropriate environment. The presence of multiple monomer types is critical to sustaining the coexistence of multiple replicator types. Full article
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Open AccessArticle Stability toward High Energy Radiation of Non-Proteinogenic Amino Acids: Implications for the Origins of Life
Life 2013, 3(3), 449-473; doi:10.3390/life3030449
Received: 8 May 2013 / Revised: 15 May 2013 / Accepted: 10 July 2013 / Published: 30 July 2013
Cited by 3 | PDF Full-text (671 KB) | HTML Full-text | XML Full-text
Abstract
A series of non-proteinogenic amino acids, most of them found quite commonly in the meteorites known as carbonaceous chondrites, were subjected to solid state radiolysis in vacuum to a total radiation dose of 3.2 MGy corresponding to 23% of the total dose [...] Read more.
A series of non-proteinogenic amino acids, most of them found quite commonly in the meteorites known as carbonaceous chondrites, were subjected to solid state radiolysis in vacuum to a total radiation dose of 3.2 MGy corresponding to 23% of the total dose expected to be taken by organic molecules buried in asteroids and meteorites since the beginning of the solar system 4.6 × 109 years ago. The radiolyzed amino acids were studied by FT-IR spectroscopy, Differential Scanning Calorimetry (DSC) and by polarimety and Optical Rotatory Dispersion (ORD). It is shown that an important fraction of each amino acid is able to “survive” the massive dose of radiation, while the enantiomeric excess is partially preserved. Based on the results obtained, it is concluded that it is unsurprising to find amino acids even in enantiomeric excess in carbonaceous chondrites. Full article
(This article belongs to the Special Issue Planet Formation and the Rise of Life)
Open AccessArticle Model of Biological Quantum Logic in DNA
Life 2013, 3(3), 474-481; doi:10.3390/life3030474
Received: 3 June 2013 / Revised: 4 July 2013 / Accepted: 19 July 2013 / Published: 2 August 2013
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Abstract
The DNA molecule has properties that allow it to act as a quantum logic processor. It has been demonstrated that there is coherent conduction of electrons longitudinally along the DNA molecule through pi stacking interactions of the aromatic nucleotide bases, and it [...] Read more.
The DNA molecule has properties that allow it to act as a quantum logic processor. It has been demonstrated that there is coherent conduction of electrons longitudinally along the DNA molecule through pi stacking interactions of the aromatic nucleotide bases, and it has also been demonstrated that electrons moving longitudinally along the DNA molecule are subject to a very efficient electron spin filtering effect as the helicity of the DNA molecule interacts with the spin of the electron. This means that, in DNA, electrons are coherently conducted along a very efficient spin filter. Coherent electron spin is held in a logically and thermodynamically reversible chiral symmetry between the C2-endo and C3-endo enantiomers of the deoxyribose moiety in each nucleotide, which enables each nucleotide to function as a quantum gate. The symmetry break that provides for quantum decision in the system is determined by the spin direction of an electron that has an orbital angular momentum that is sufficient to overcome the energy barrier of the double well potential separating the C2-endo and C3-endo enantiomers, and that enantiomeric energy barrier is appropriate to the Landauer limit of the energy necessary to randomize one bit of information. Full article
Open AccessArticle Natural Pyrrhotite as a Catalyst in Prebiotic Chemical Evolution
Life 2013, 3(3), 502-517; doi:10.3390/life3030502
Received: 3 June 2013 / Revised: 19 August 2013 / Accepted: 20 August 2013 / Published: 28 August 2013
PDF Full-text (428 KB) | HTML Full-text | XML Full-text
Abstract
The idea of an autotrophic organism as the first living being on Earth leads to the hypothesis of a protometabolic, complex chemical system. In one of the main hypotheses, the first metabolic systems emerged from the interaction between sulfide minerals and/or soluble [...] Read more.
The idea of an autotrophic organism as the first living being on Earth leads to the hypothesis of a protometabolic, complex chemical system. In one of the main hypotheses, the first metabolic systems emerged from the interaction between sulfide minerals and/or soluble iron-sulfide complexes and fluids rich in inorganic precursors, which are reduced and derived from crustal or mantle activity. Within this context, the possible catalytic role of pyrrhotite, one of the most abundant sulfide minerals, in biomimetic redox and carbon fixation reactions was studied. Our results showed that pyrrhotite, under simulated hydrothermal conditions, could catalyze the pyruvate synthesis from lactate and that a dynamic system formed by coupling iron metal and iron-sulfur species in an electrochemical cell could promote carbon fixation from thioacetate esters. Full article

Review

Jump to: Editorial, Research

Open AccessReview Eukaryotic Organisms in Extreme Acidic Environments, the Río Tinto Case
Life 2013, 3(3), 363-374; doi:10.3390/life3030363
Received: 12 March 2013 / Revised: 7 June 2013 / Accepted: 17 June 2013 / Published: 4 July 2013
Cited by 6 | PDF Full-text (630 KB) | HTML Full-text | XML Full-text
Abstract
A major issue in microbial ecology is to identify the limits of life for growth and survival, and to understand the molecular mechanisms that define these limits. Thus, interest in the biodiversity and ecology of extreme environments has grown in recent years [...] Read more.
A major issue in microbial ecology is to identify the limits of life for growth and survival, and to understand the molecular mechanisms that define these limits. Thus, interest in the biodiversity and ecology of extreme environments has grown in recent years for several reasons. Some are basic and revolve around the idea that extreme environments are believed to reflect early Earth conditions. Others are related to the biotechnological potential of extremophiles. In this regard, the study of extremely acidic environments has become increasingly important since environmental acidity is often caused by microbial activity. Highly acidic environments are relatively scarce worldwide and are generally associated with volcanic activity or mining operations. For most acidic environments, low pH facilitates metal solubility, and therefore acidic waters tend to have high concentrations of heavy metals. However, highly acidic environments are usually inhabited by acidophilic and acidotolerant eukaryotic microorganisms such as algae, amoebas, ciliates, heliozoan and rotifers, not to mention filamentous fungi and yeasts. Here, we review the general trends concerning the diversity and ecophysiology of eukaryotic acidophilic microorganims, as well as summarize our latest results on this topic in one of the largest extreme acidic rivers, Río Tinto (SW, Spain). Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Open AccessReview Domain Structures and Inter-Domain Interactions Defining the Holoenzyme Architecture of Archaeal D-Family DNA Polymerase
Life 2013, 3(3), 375-385; doi:10.3390/life3030375
Received: 15 April 2013 / Revised: 26 June 2013 / Accepted: 27 June 2013 / Published: 5 July 2013
PDF Full-text (660 KB) | HTML Full-text | XML Full-text
Abstract
Archaea-specific D-family DNA polymerase (PolD) forms a dimeric heterodimer consisting of two large polymerase subunits and two small exonuclease subunits. According to the protein-protein interactions identified among the domains of large and small subunits of PolD, a symmetrical model for the domain [...] Read more.
Archaea-specific D-family DNA polymerase (PolD) forms a dimeric heterodimer consisting of two large polymerase subunits and two small exonuclease subunits. According to the protein-protein interactions identified among the domains of large and small subunits of PolD, a symmetrical model for the domain topology of the PolD holoenzyme is proposed. The experimental evidence supports various aspects of the model. The conserved amphipathic nature of the N-terminal putative α-helix of the large subunit plays a key role in the homodimeric assembly and the self-cyclization of the large subunit and is deeply involved in the archaeal PolD stability and activity. We also discuss the evolutional transformation from archaeal D-family to eukaryotic B-family polymerase on the basis of the structural information. Full article
(This article belongs to the Special Issue Extremophiles and Extreme Environments)
Open AccessReview Simple Organics and Biomonomers Identified in HCN Polymers: An Overview
Life 2013, 3(3), 421-448; doi:10.3390/life3030421
Received: 15 April 2013 / Revised: 18 June 2013 / Accepted: 28 June 2013 / Published: 29 July 2013
Cited by 5 | PDF Full-text (275 KB) | HTML Full-text | XML Full-text
Abstract
Hydrogen cyanide (HCN) is a ubiquitous molecule in the Universe. It is a compound that is easily produced in significant yields in prebiotic simulation experiments using a reducing atmosphere. HCN can spontaneously polymerise under a wide set of experimental conditions. It has [...] Read more.
Hydrogen cyanide (HCN) is a ubiquitous molecule in the Universe. It is a compound that is easily produced in significant yields in prebiotic simulation experiments using a reducing atmosphere. HCN can spontaneously polymerise under a wide set of experimental conditions. It has even been proposed that HCN polymers could be present in objects such as asteroids, moons, planets and, in particular, comets. Moreover, it has been suggested that these polymers could play an important role in the origin of life. In this review, the simple organics and biomonomers that have been detected in HCN polymers, the analytical techniques and procedures that have been used to detect and characterise these molecules and an exhaustive classification of the experimental/environmental conditions that favour the formation of HCN polymers are summarised. Nucleobases, amino acids, carboxylic acids, cofactor derivatives and other compounds have been identified in HCN polymers. The great molecular diversity found in HCN polymers encourages their placement at the central core of a plausible protobiological system. Full article
Open AccessReview Formaldehyde—A Key Monad of the Biomolecular System
Life 2013, 3(3), 486-501; doi:10.3390/life3030486
Received: 2 May 2013 / Revised: 17 July 2013 / Accepted: 30 July 2013 / Published: 16 August 2013
PDF Full-text (295 KB) | HTML Full-text | XML Full-text
Abstract
Experiments will be presented and reviewed to support the hypothesis that the intrinsic reactivity of formaldehyde may lead to the formation of a rather comprehensive set of defined biomolecules, including D-glucose, thus fostering concepts of evolution considering the existence of a premetabolic [...] Read more.
Experiments will be presented and reviewed to support the hypothesis that the intrinsic reactivity of formaldehyde may lead to the formation of a rather comprehensive set of defined biomolecules, including D-glucose, thus fostering concepts of evolution considering the existence of a premetabolic system as a primordial step in the generation of life. Full article

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