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Life, Volume 9, Issue 3 (September 2019) – 23 articles

Cover Story (view full-size image): Across the domains of life, a nearly universal genetic code underlies the translation of genetic information into proteins. In select cases, this universal code is slightly altered to encode amino acids beyond the standard 20, thus expanding the genetic code. In recent decades, methods have been developed for artificially expanding the genetic code to incorporate nonstandard amino acids. However, orthogonality between native and artificially introduced translational system components has been a longstanding issue. Novel approaches to enhance this orthogonality include the development of optimized orthogonal translation systems, orthogonal tethered ribosomes, and the recoding of genomes to fundamentally alter the genetic code. View this paper.
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Essay
The Naked Mole-Rat: An Unusual Organism with an Unexpected Latent Potential for Increased Intelligence?
Life 2019, 9(3), 76; https://doi.org/10.3390/life9030076 - 16 Sep 2019
Cited by 3 | Viewed by 4438
Abstract
Naked mole-rats are eusocial, hairless mammals that are uniquely adapted to their harsh, low-oxygen subsurface habitat. Although their encephalization quotient, a controversial marker of intelligence, is low, they exhibit many features considered tell-tale signs of highly intelligent species on our planet including longevity, [...] Read more.
Naked mole-rats are eusocial, hairless mammals that are uniquely adapted to their harsh, low-oxygen subsurface habitat. Although their encephalization quotient, a controversial marker of intelligence, is low, they exhibit many features considered tell-tale signs of highly intelligent species on our planet including longevity, plasticity, social cohesion and interaction, rudimentary language, sustainable farming abilities, and maintaining sanitary conditions in their self-built complex housing structures. It is difficult to envision how naked mole-rats would reach even higher levels of intelligence in their natural sensory-challenged habitat, but such an evolutionary path cannot be excluded if they would expand their range onto the earth’s surface. Full article
(This article belongs to the Section Astrobiology)
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Article
Prebiotic Peptide Bond Formation Through Amino Acid Phosphorylation. Insights from Quantum Chemical Simulations
Life 2019, 9(3), 75; https://doi.org/10.3390/life9030075 - 16 Sep 2019
Cited by 7 | Viewed by 4396
Abstract
Condensation reactions between biomolecular building blocks are the main synthetic channels to build biopolymers. However, under highly diluted prebiotic conditions, condensations are thermodynamically hampered since they release water. Moreover, these reactions are also kinetically hindered as, in the absence of any catalyst, they [...] Read more.
Condensation reactions between biomolecular building blocks are the main synthetic channels to build biopolymers. However, under highly diluted prebiotic conditions, condensations are thermodynamically hampered since they release water. Moreover, these reactions are also kinetically hindered as, in the absence of any catalyst, they present high activation energies. In living organisms, in the formation of peptides by condensation of amino acids, this issue is overcome by the participation of adenosine triphosphate (ATP), in which, previous to the condensation, phosphorylation of one of the reactants is carried out to convert it as an activated intermediate. In this work, we present for the first time results based on density functional theory (DFT) calculations on the peptide bond formation between two glycine (Gly) molecules adopting this phosphorylation-based mechanism considering a prebiotic context. Here, ATP has been modeled by a triphosphate (TP) component, and different scenarios have been considered: (i) gas-phase conditions, (ii) in the presence of a Mg2+ ion available within the layer of clays, and (iii) in the presence of a Mg2+ ion in watery environments. For all of them, the free energy profiles have been fully characterized. Energetics derived from the quantum chemical calculations indicate that none of the processes seem to be feasible in the prebiotic context. In scenarios (i) and (ii), the reactions are inhibited due to unfavorable thermodynamics associated with the formation of high energy intermediates, while in scenario (iii), the reaction is inhibited due to the high free energy barrier associated with the condensation reactions. As a final consideration, the role of clays in this TP-mediated peptide bond formation route is advocated, since the interaction of the phosphorylated intermediate with the internal clay surfaces could well favor the reaction free energies. Full article
(This article belongs to the Section Origin of Life)
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Article
Computing the Parameter Values for the Emergence of Homochirality in Complex Networks
Life 2019, 9(3), 74; https://doi.org/10.3390/life9030074 - 15 Sep 2019
Viewed by 1539
Abstract
The goal of our research is the development of algorithmic tools for the analysis of chemical reaction networks proposed as models of biological homochirality. We focus on two algorithmic problems: detecting whether or not a chemical mechanism admits mirror symmetry-breaking; and, given one [...] Read more.
The goal of our research is the development of algorithmic tools for the analysis of chemical reaction networks proposed as models of biological homochirality. We focus on two algorithmic problems: detecting whether or not a chemical mechanism admits mirror symmetry-breaking; and, given one of those networks as input, sampling the set of racemic steady states that can produce mirror symmetry-breaking. Algorithmic solutions to those two problems will allow us to compute the parameter values for the emergence of homochirality. We found a mathematical criterion for the occurrence of mirror symmetry-breaking. This criterion allows us to compute semialgebraic definitions of the sets of racemic steady states that produce homochirality. Although those semialgebraic definitions can be processed algorithmically, the algorithmic analysis of them becomes unfeasible in most cases, given the nonlinear character of those definitions. We use Clarke’s system of convex coordinates to linearize, as much as possible, those semialgebraic definitions. As a result of this work, we get an efficient algorithm that solves both algorithmic problems for networks containing only one enantiomeric pair and a heuristic algorithm that can be used in the general case, with two or more enantiomeric pairs. Full article
(This article belongs to the Special Issue The Origin of Chirality in Life (Chiral Symmetry Breaking))
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Editorial
The Origin and Early Evolution of Life: Prebiotic Chemistry
Life 2019, 9(3), 73; https://doi.org/10.3390/life9030073 - 12 Sep 2019
Cited by 8 | Viewed by 1920
Abstract
Microfossil evidence indicates that cellular life on Earth emerged during the Paleoarchean era be-tween 3 [...] Full article
Article
Characterizing Interstellar Medium, Planetary Surface and Deep Environments by Spectroscopic Techniques Using Unique Simulation Chambers at Centro de Astrobiologia (CAB)
Life 2019, 9(3), 72; https://doi.org/10.3390/life9030072 - 10 Sep 2019
Cited by 1 | Viewed by 1786
Abstract
At present, the study of diverse habitable environments of astrobiological interest has become a major challenge. Due to the obvious technical and economical limitations on in situ exploration, laboratory simulations are one of the most feasible research options to make advances both in [...] Read more.
At present, the study of diverse habitable environments of astrobiological interest has become a major challenge. Due to the obvious technical and economical limitations on in situ exploration, laboratory simulations are one of the most feasible research options to make advances both in several astrobiologically interesting environments and in developing a consistent description of the origin of life. With this objective in mind, we applied vacuum and high pressure technology to the design of versatile simulation chambers devoted to the simulation of the interstellar medium, planetary atmospheres conditions and high-pressure environments. These simulation facilities are especially appropriate for studying the physical, chemical and biological changes induced in a particular sample by in situ irradiation or physical parameters in a controlled environment. Furthermore, the implementation of several spectroscopies, such as infrared, Raman, ultraviolet, etc., to study solids, and mass spectrometry to monitor the gas phase, in our simulation chambers, provide specific tools for the in situ physico-chemical characterization of analogues of astrobiological interest. Simulation chamber facilities are a promising and potential tool for planetary exploration of habitable environments. A review of many wide-ranging applications in astrobiology are detailed herein to provide an understanding of the potential and flexibility of these unique experimental systems. Full article
(This article belongs to the Special Issue Planetary Exploration of Habitable Environments)
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Review
The Vulnerability of Microbial Ecosystems in a Changing Climate: Potential Impact in Shark Bay
Life 2019, 9(3), 71; https://doi.org/10.3390/life9030071 - 02 Sep 2019
Cited by 8 | Viewed by 2659
Abstract
The potential impact of climate change on eukaryotes, including humans, has been relatively well described. In contrast, the contribution and susceptibility of microorganisms to a changing climate have, until recently, received relatively less attention. In this review, the importance of microorganisms in the [...] Read more.
The potential impact of climate change on eukaryotes, including humans, has been relatively well described. In contrast, the contribution and susceptibility of microorganisms to a changing climate have, until recently, received relatively less attention. In this review, the importance of microorganisms in the climate change discourse is highlighted. Microorganisms are responsible for approximately half of all primary production on earth, support all forms of macroscopic life whether directly or indirectly, and often persist in “extreme” environments where most other life are excluded. In short, microorganisms are the life support system of the biosphere and therefore must be included in decision making regarding climate change. Any effects climate change will have on microorganisms will inevitably impact higher eukaryotes and the activity of microbial communities in turn can contribute to or alleviate the severity of the changing climate. It is of vital importance that unique, fragile, microbial ecosystems are a focus of research efforts so that their resilience to extreme weather events and climate change are thoroughly understood and that conservation efforts can be implemented as a response. One such ecosystem under threat are the evolutionarily significant microbial mats and stromatolites, such as those present in Shark Bay, Western Australia. Climate change models have suggested the duration and severity of extreme weather events in this region will increase, along with rising temperatures, sea levels, and ocean acidification. These changes could upset the delicate balance that fosters the development of microbial mats and stromatolites in Shark Bay. Thus, the challenges facing Shark Bay microbial communities will be presented here as a specific case study. Full article
(This article belongs to the Section Microbiology)
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Article
The Oxygen Release Instrument: Space Mission Reactive Oxygen Species Measurements for Habitability Characterization, Biosignature Preservation Potential Assessment, and Evaluation of Human Health Hazards
Life 2019, 9(3), 70; https://doi.org/10.3390/life9030070 - 27 Aug 2019
Viewed by 1857
Abstract
We describe the design of an instrument, the OxR (for Oxygen Release), for the enzymatically specific and non-enzymatic detection and quantification of the reactive oxidant species (ROS), superoxide radicals (O2•−), and peroxides (O22−, e.g., H2O [...] Read more.
We describe the design of an instrument, the OxR (for Oxygen Release), for the enzymatically specific and non-enzymatic detection and quantification of the reactive oxidant species (ROS), superoxide radicals (O2•−), and peroxides (O22−, e.g., H2O2) on the surface of Mars and Moon. The OxR instrument is designed to characterize planetary habitability, evaluate human health hazards, and identify sites with high biosignature preservation potential. The instrument can also be used for missions to the icy satellites of Saturn’s Titan and Enceladus, and Jupiter’s Europa. The principle of the OxR instrument is based on the conversion of (i) O2•− to O2 via its enzymatic dismutation (which also releases H2O2), and of (ii) H2O2 (free or released by the hydrolysis of peroxides and by the dismutation of O2•−) to O2 via enzymatic decomposition. At stages i and ii, released O2 is quantitatively detected by an O2 sensor and stoichiometrically converted to moles of O2•− and H2O2. A non-enzymatic alternative approach is also designed. These methods serve as the design basis for the construction of a new small-footprint instrument for specific oxidant detection. The minimum detection limit of the OxR instrument for O2•− and O22− in Mars, Lunar, and Titan regolith, and in Europa and Enceladus ice is projected to be 10 ppb. The methodology of the OxR instrument can be rapidly advanced to flight readiness by leveraging the Phoenix Wet Chemical Laboratory, or microfluidic sample processing technologies. Full article
(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)
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Article
Origin of the Genetic Code Is Found at the Transition between a Thioester World of Peptides and the Phosphoester World of Polynucleotides
Life 2019, 9(3), 69; https://doi.org/10.3390/life9030069 - 22 Aug 2019
Cited by 20 | Viewed by 2923
Abstract
The early metabolism arising in a Thioester world gave rise to amino acids and their simple peptides. The catalytic activity of these early simple peptides became instrumental in the transition from Thioester World to a Phosphate World. This transition involved the appearances of [...] Read more.
The early metabolism arising in a Thioester world gave rise to amino acids and their simple peptides. The catalytic activity of these early simple peptides became instrumental in the transition from Thioester World to a Phosphate World. This transition involved the appearances of sugar phosphates, nucleotides, and polynucleotides. The coupling of the amino acids and peptides to nucleotides and polynucleotides is the origin for the genetic code. Many of the key steps in this transition are seen in the catalytic cores of the nucleotidyltransferases, the class II tRNA synthetases (aaRSs) and the CCA adding enzyme. These catalytic cores are dominated by simple beta hairpin structures formed in the Thioester World. The code evolved from a proto-tRNA, a tetramer XCCA interacting with a proto-aminoacyl-tRNA synthetase (aaRS) activating Glycine and Proline. The initial expanded code is found in the acceptor arm of the tRNA, the operational code. It is the coevolution of the tRNA with the aaRSs that is at the heart of the origin and evolution of the genetic code. There is also a close relationship between the accretion models of the evolving tRNA and that of the ribosome. Full article
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Article
Sustainable Growth and Synchronization in Protocell Models
Life 2019, 9(3), 68; https://doi.org/10.3390/life9030068 - 21 Aug 2019
Cited by 6 | Viewed by 1515
Abstract
The growth of a population of protocells requires that the two key processes of replication of the protogenetic material and reproduction of the whole protocell take place at the same rate. While in many ODE-based models such synchronization spontaneously develops, this does not [...] Read more.
The growth of a population of protocells requires that the two key processes of replication of the protogenetic material and reproduction of the whole protocell take place at the same rate. While in many ODE-based models such synchronization spontaneously develops, this does not happen in the important case of quadratic growth terms. Here we show that spontaneous synchronization can be recovered (i) by requiring that the transmembrane diffusion of precursors takes place at a finite rate, or (ii) by introducing a finite lifetime of the molecular complexes. We then consider reaction networks that grow by the addition of newly synthesized chemicals in a binary polymer model, and analyze their behaviors in growing and dividing protocells, thereby confirming the importance of (i) and (ii) for synchronization. We describe some interesting phenomena (like long-term oscillations of duplication times) and show that the presence of food-generated autocatalytic cycles is not sufficient to guarantee synchronization: in the case of cycles with a complex structure, it is often observed that only some subcycles survive and synchronize, while others die out. This shows the importance of truly dynamic models that can uncover effects that cannot be detected by static graph theoretical analyses. Full article
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Review
Universal Molecular Triggers of Stress Responses in Cyanobacterium Synechocystis
Life 2019, 9(3), 67; https://doi.org/10.3390/life9030067 - 20 Aug 2019
Cited by 14 | Viewed by 2211
Abstract
Systemic analysis of stress-induced transcription in the cyanobacterium Synechocystis sp. strain PCC 6803 identifies a number of genes as being induced in response to most abiotic stressors (heat, osmotic, saline, acid stress, strong light, and ultraviolet radiation). Genes for heat-shock proteins (HSPs) are [...] Read more.
Systemic analysis of stress-induced transcription in the cyanobacterium Synechocystis sp. strain PCC 6803 identifies a number of genes as being induced in response to most abiotic stressors (heat, osmotic, saline, acid stress, strong light, and ultraviolet radiation). Genes for heat-shock proteins (HSPs) are activated by all these stresses and form a group that universally responds to all environmental changes. The functions of universal triggers of stress responses in cyanobacteria can be performed by reactive oxygen species (ROS), in particular H2O2, as well as changes in the redox potential of the components of the photosynthetic electron transport chain. The double mutant of Synechocystis sp. PCC 6803 (katG/tpx, or sll1987/sll0755), which is defective in antioxidant enzymes catalase (KatG) and thioredoxin peroxidase (Tpx), cannot grow in the presence of exogenous hydrogen peroxide (H2O2); and it is extremely sensitive to low concentrations of H2O2, especially under conditions of cold stress. Experiments on this mutant demonstrate that H2O2 is involved in regulation of gene expression that responds to a decrease in ambient temperature, and affects both the perception and the signal transduction of cold stress. In addition, they suggest that formation of ROS largely depends on the physical state of the membranes such as fluidity or viscosity. In cyanobacteria, an increase in membrane turnover leads to a decrease in the formation of ROS and an increase in resistance to cold stress. Therefore: (1) H2O2 is the universal trigger of stress responses in cyanobacterial cells; (2) ROS formation (in particular, H2O2) depends on the physical properties of both cytoplasmic and thylakoid membranes; (3) The destructive effect of H2O2 is reduced by increasing of fluidity of biological membranes. Full article
(This article belongs to the Section Microbiology)
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Essay
The Informational Substrate of Chemical Evolution: Implications for Abiogenesis
Life 2019, 9(3), 66; https://doi.org/10.3390/life9030066 - 08 Aug 2019
Cited by 3 | Viewed by 2747
Abstract
A key aspect of biological evolution is the capacity of living systems to process information, coded in deoxyribonucleic acid (DNA), and used to direct how the cell works. The overall picture that emerges today from fields such as developmental, synthetic, and systems biology [...] Read more.
A key aspect of biological evolution is the capacity of living systems to process information, coded in deoxyribonucleic acid (DNA), and used to direct how the cell works. The overall picture that emerges today from fields such as developmental, synthetic, and systems biology indicates that information processing in cells occurs through a hierarchy of genes regulating the activity of other genes through complex metabolic networks. There is an implicit semiotic character in this way of dealing with information, based on functional molecules that act as signs to achieve self-regulation of the whole network. In contrast to cells, chemical systems are not thought of being able to process information, yet they must have preceded biological organisms, and evolved into them. Hence, there must have been prebiotic molecular assemblies that could somehow process information, in order to regulate their own constituent reactions and supramolecular organization processes. The purpose of this essay is then to reflect about the distinctive features of information in living and non-living matter, and on how the capacity of biological organisms for information processing was possibly rooted in a particular type of chemical systems (here referred to as autonomous chemical systems), which could self-sustain and reproduce through organizational closure of their molecular building blocks. Full article
(This article belongs to the Special Issue Modelling Life-Like Behavior in Systems Chemistry)
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Article
Survival of RNA Replicators Is Much Easier in Protocells Than in Surface-Based, Spatial Systems
Life 2019, 9(3), 65; https://doi.org/10.3390/life9030065 - 07 Aug 2019
Cited by 10 | Viewed by 1984
Abstract
In RNA-World scenarios for the origin of life, replication is catalyzed by polymerase ribozymes. Replicating RNA systems are subject to invasion by non-functional parasitic strands. It is well-known that there are two ways to avoid the destruction of the system by parasites: spatial [...] Read more.
In RNA-World scenarios for the origin of life, replication is catalyzed by polymerase ribozymes. Replicating RNA systems are subject to invasion by non-functional parasitic strands. It is well-known that there are two ways to avoid the destruction of the system by parasites: spatial clustering in models with limited diffusion, or group selection in protocells. Here, we compare computational models of replication in spatial models and protocells as closely as possible in order to determine the relative importance of these mechanisms in the RNA World. For the survival of the polymerases, the replication rate must be greater than a minimum threshold value, kmin, and the mutation rate in replication must be less than a maximum value, Mmax, which is known as the error threshold. For the protocell models, we find that kmin is substantially lower and Mmax is substantially higher than for the equivalent spatial models; thus, the survival of polymerases is much easier in protocells than on surfaces. The results depend on the maximum number of strands permitted in one protocell or one lattice site in the spatial model, and on whether replication is limited by the supply of monomers or the population size of protocells. The substantial advantages that are seen in the protocell models relative to the spatial models are robust to changing these details. Thus, cooperative polymerases with limited accuracy would have found it much easier to operate inside lipid compartments, and this suggests that protocells may have been a very early step in the development of life. We consider cases where parasites have an equal replication rate to polymerases, and cases where parasites multiply twice as fast as polymerases. The advantage of protocell models over spatial models is increased when the parasites multiply faster. Full article
(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)
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Article
Productivity and Community Composition of Low Biomass/High Silica Precipitation Hot Springs: A Possible Window to Earth’s Early Biosphere?
Life 2019, 9(3), 64; https://doi.org/10.3390/life9030064 - 29 Jul 2019
Cited by 5 | Viewed by 1656
Abstract
Terrestrial hot springs have provided a niche space for microbial communities throughout much of Earth’s history, and evidence for hydrothermal deposits on the Martian surface suggest this could have also been the case for the red planet. Prior to the evolution of photosynthesis, [...] Read more.
Terrestrial hot springs have provided a niche space for microbial communities throughout much of Earth’s history, and evidence for hydrothermal deposits on the Martian surface suggest this could have also been the case for the red planet. Prior to the evolution of photosynthesis, life in hot springs on early Earth would have been supported though chemoautotrophy. Today, hot spring geochemical and physical parameters can preclude the occurrence of oxygenic phototrophs, providing an opportunity to characterize the geochemical and microbial components. In the absence of the photo-oxidation of water, chemoautotrophy in these hot springs (and throughout Earth’s history) relies on the delivery of exogenous electron acceptors and donors such as H2, H2S, and Fe2+. Thus, systems fueled by chemoautotrophy are likely energy substrate-limited and support low biomass communities compared to those where oxygenic phototrophs are prevalent. Low biomass silica-precipitating systems have implications for preservation, especially over geologic time. Here, we examine and compare the productivity and composition of low biomass chemoautotrophic versus photoautotrophic communities in silica-saturated hot springs. Our results indicate low biomass chemoautotrophic microbial communities in Yellowstone National Park are supported primarily by sulfur redox reactions and, while similar in total biomass, show higher diversity in anoxygenic phototrophic communities compared to chemoautotrophs. Our data suggest productivity in Archean terrestrial hot springs may be directly linked to redox substrate availability, and there may be high potential for geochemical and physical biosignature preservation from these communities. Full article
(This article belongs to the Special Issue Water–Rock Interactions and Life)
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Article
Modelling Bacteria-Inspired Dynamics with Networks of Interacting Chemicals
Life 2019, 9(3), 63; https://doi.org/10.3390/life9030063 - 29 Jul 2019
Cited by 5 | Viewed by 1996
Abstract
One approach to understanding how life-like properties emerge involves building synthetic cellular systems that mimic certain dynamical features of living cells such as bacteria. Here, we developed a model of a reaction network in a cellular system inspired by the ability of bacteria [...] Read more.
One approach to understanding how life-like properties emerge involves building synthetic cellular systems that mimic certain dynamical features of living cells such as bacteria. Here, we developed a model of a reaction network in a cellular system inspired by the ability of bacteria to form a biofilm in response to increasing cell density. Our aim was to determine the role of chemical feedback in the dynamics. The feedback was applied through the enzymatic rate dependence on pH, as pH is an important parameter that controls the rates of processes in cells. We found that a switch in pH can be used to drive base-catalyzed gelation or precipitation of a substance in the external solution. A critical density of cells was required for gelation that was essentially independent of the pH-driven feedback. However, the cell pH reached a higher maximum as a result of the appearance of pH oscillations with feedback. Thus, we conclude that while feedback may not play a vital role in some density-dependent behavior in cellular systems, it nevertheless can be exploited to activate internally regulated cell processes at low cell densities. Full article
(This article belongs to the Special Issue Modelling Life-Like Behavior in Systems Chemistry)
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Review
New Applications of High-Resolution Analytical Methods to Study Trace Organic Compounds in Extraterrestrial Materials
Life 2019, 9(3), 62; https://doi.org/10.3390/life9030062 - 26 Jul 2019
Cited by 4 | Viewed by 1780
Abstract
Organic compounds are present as complex mixtures in extraterrestrial materials including meteorites, which may have played important roles in the origin of life on the primitive Earth. However, the distribution and formation mechanisms of meteoritic organic compounds are not well understood, because conventional [...] Read more.
Organic compounds are present as complex mixtures in extraterrestrial materials including meteorites, which may have played important roles in the origin of life on the primitive Earth. However, the distribution and formation mechanisms of meteoritic organic compounds are not well understood, because conventional analytical methods have limited resolution and sensitivity to resolve their molecular complexity. In this study, advanced instrumental development and analyses are proposed in order to study the trace organic compounds of extraterrestrial materials: (1) a clean room environment to avoid organic contamination during analysis; (2) high-mass-resolution analysis (up to ~150,000 m/Δm) coupled with high-performance liquid chromatography (HPLC) in order to determine the elemental composition using exact mass for inferring the chemical structure; (3) superior chromatographic separation using a two-dimensional system in order to determine the structural and optical isomers of amino acids; and (4) in situ organic compound analysis and molecular imaging of the sample surface. This approach revealed a higher complexity of organic compounds with a heterogeneous distribution in meteorites. These new methods can be applied to study the chemical evolution of meteoritic organic compounds as well as the molecular occurrence in very-low-mass extraterrestrial materials such as asteroid-returned samples. Full article
(This article belongs to the Special Issue Analytical Chemistry in Astrobiology)
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Article
Cultivar-Specific Performance and Qualitative Descriptors for Butterhead Salanova Lettuce Produced in Closed Soilless Cultivation as a Candidate Salad Crop for Human Life Support in Space
Life 2019, 9(3), 61; https://doi.org/10.3390/life9030061 - 14 Jul 2019
Cited by 19 | Viewed by 2529
Abstract
Plant production is crucial for space journeys self-autonomy by contributing to the dietary intake necessary to sustain the physical and psychological well-being of space colonists, as well as for contributing to atmospheric revitalization, water purification and waste product recycling. Choosing the appropriate cultivar [...] Read more.
Plant production is crucial for space journeys self-autonomy by contributing to the dietary intake necessary to sustain the physical and psychological well-being of space colonists, as well as for contributing to atmospheric revitalization, water purification and waste product recycling. Choosing the appropriate cultivar is equally important as the species selection, since cultivar influences the obtained fresh biomass, water use efficiency (WUE), growing cycle duration, qualitative features and postharvest performance. Two differently pigmented butterhead Lactuca sativa L. (red and green Salanova) cultivars were assessed in terms of morphometric, mineral, bioactive and physiological parameters. The experiment was carried out in a controlled environment growth chamber using a closed soilless system (nutrient film technique). Red Salanova registered a biomass of 130 g at harvest, which was 22.1% greater than green Salanova, and a water uptake of 1.42 L during the full growing period corresponding to WUE of 91.9 g L−1, which was 13.8% higher than that of green Salanova. At harvest, green Salanova had accumulated more P, K, Ca, Mg and 37.2% more nitrate than red Salanova, which however had higher relative water content, leaf total and osmotic potential and higher SPAD index. Red Salanova also exhibited at harvest around two-fold higher lipophilic antioxidant activity and total phenols, and around six-fold higher total ascorbic acid levels. These latter characteristics improved the antioxidant capacity of red Salanova enabling it to use light more efficiently and deliver better overall performance and yield than green Salanova. Moreover, the higher phenolics and total ascorbic acid contents of red Salanova constitute natural sources of antioxidants for enriching the human diet and render it an optimal candidate cultivar for near-term missions. Full article
(This article belongs to the Section Astrobiology)
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Essay
The Essence of Systems Chemistry
Life 2019, 9(3), 60; https://doi.org/10.3390/life9030060 - 11 Jul 2019
Cited by 4 | Viewed by 2166
Abstract
Systems Chemistry investigates the upkeep of specific interactions of an exceptionally broad choice of objects over longer periods of time than the average time of existence of the objects themselves. This maintenance of a dynamic state focuses on conditions where the objects are [...] Read more.
Systems Chemistry investigates the upkeep of specific interactions of an exceptionally broad choice of objects over longer periods of time than the average time of existence of the objects themselves. This maintenance of a dynamic state focuses on conditions where the objects are thermodynamically not very stable and should be rare or virtually inexistent. It does not matter whether they are homochirally enriched populations of chiral molecules, a specific composition of some sort of aggregate, supramolecules, or even a set of chemically relatively unstable molecules that constantly transform one into another. What does matter is that these specific interactions prevail in complex mixtures and eventually grow in numbers and frequency through the enhancing action of autocatalysis, which makes such systems ultimately resemble living cells and interacting living populations. Such chemical systems need to be correctly understood, but also intuitively described. They may be so complex that metaphors become practically more important, as a means of communication, than the precise and correct technical description of chemical models and complex molecular or supramolecular relations. This puts systems chemists on a tightrope walk of science communication, between the complex reality and an imaginative model world. This essay addresses, both, scientists who would like to read “A Brief History of Systems Chemistry”, that is, about its “essence”, and systems chemists who work with and communicate complex life-like chemical systems. I illustrate for the external reader a light mantra, that I call “to make more of it”, and I charily draw systems chemists to reflect upon the fact that chemists are not always good at drawing a clear line between a model and “the reality”: The real thing. We are in a constant danger of taking metaphors for real. Yet in real life, we do know very well that we cannot smoke with Magritte’s pipe, don’t we? Full article
(This article belongs to the Special Issue Modelling Life-Like Behavior in Systems Chemistry)
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Review
Synthetic Approaches for Nucleic Acid Delivery: Choosing the Right Carriers
Life 2019, 9(3), 59; https://doi.org/10.3390/life9030059 - 09 Jul 2019
Cited by 35 | Viewed by 3308
Abstract
The discovery of the genetic roots of various human diseases has motivated the exploration of different exogenous nucleic acids as therapeutic agents to treat these genetic disorders (inherited or acquired). However, the physicochemical properties of nucleic acids render them liable to degradation and [...] Read more.
The discovery of the genetic roots of various human diseases has motivated the exploration of different exogenous nucleic acids as therapeutic agents to treat these genetic disorders (inherited or acquired). However, the physicochemical properties of nucleic acids render them liable to degradation and also restrict their cellular entrance and gene translation/inhibition at the correct cellular location. Therefore, gene condensation/protection and guided intracellular trafficking are necessary for exogenous nucleic acids to function inside cells. Diversified cationic formulation materials, including natural and synthetic lipids, polymers, and proteins/peptides, have been developed to facilitate the intracellular transportation of exogenous nucleic acids. The chemical properties of different formulation materials determine their special features for nucleic acid delivery, so understanding the property–function correlation of the formulation materials will inspire the development of next-generation gene delivery carriers. Therefore, in this review, we focus on the chemical properties of different types of formulation materials and discuss how these formulation materials function as protectors and cellular pathfinders for nucleic acids, bringing them to their destination by overcoming different cellular barriers. Full article
(This article belongs to the Special Issue Modelling Life-Like Behavior in Systems Chemistry)
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Concept Paper
The Role of Orthogonality in Genetic Code Expansion
Life 2019, 9(3), 58; https://doi.org/10.3390/life9030058 - 05 Jul 2019
Cited by 13 | Viewed by 2774
Abstract
The genetic code defines how information in the genome is translated into protein. Aside from a handful of isolated exceptions, this code is universal. Researchers have developed techniques to artificially expand the genetic code, repurposing codons and translational machinery to incorporate nonstandard amino [...] Read more.
The genetic code defines how information in the genome is translated into protein. Aside from a handful of isolated exceptions, this code is universal. Researchers have developed techniques to artificially expand the genetic code, repurposing codons and translational machinery to incorporate nonstandard amino acids (nsAAs) into proteins. A key challenge for robust genetic code expansion is orthogonality; the engineered machinery used to introduce nsAAs into proteins must co-exist with native translation and gene expression without cross-reactivity or pleiotropy. The issue of orthogonality manifests at several levels, including those of codons, ribosomes, aminoacyl-tRNA synthetases, tRNAs, and elongation factors. In this concept paper, we describe advances in genome recoding, translational engineering and associated challenges rooted in establishing orthogonality needed to expand the genetic code. Full article
(This article belongs to the Special Issue Modelling Life-Like Behavior in Systems Chemistry)
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Article
Formation of Abasic Oligomers in Nonenzymatic Polymerization of Canonical Nucleotides
Life 2019, 9(3), 57; https://doi.org/10.3390/life9030057 - 04 Jul 2019
Cited by 5 | Viewed by 2427
Abstract
Polymerization of nucleotides under prebiotically plausible conditions has been a focus of several origins of life studies. Non-activated nucleotides have been shown to undergo polymerization under geothermal conditions when subjected to dry-wet cycles. They do so by a mechanism similar to acid-catalyzed ester-bond [...] Read more.
Polymerization of nucleotides under prebiotically plausible conditions has been a focus of several origins of life studies. Non-activated nucleotides have been shown to undergo polymerization under geothermal conditions when subjected to dry-wet cycles. They do so by a mechanism similar to acid-catalyzed ester-bond formation. However, one study showed that the low pH of these reactions resulted in predominantly depurination, thereby resulting in the formation of abasic sites in the oligomers. In this study, we aimed to systematically characterize the nature of the oligomers that resulted in reactions that involved one or more of the canonical ribonucleotides. All the reactions analyzed showed the presence of abasic oligomers, with purine nucleotides being affected the most due to deglycosylation. Even in the reactions that contained nucleotide mixtures, the presence of abasic oligomers was detected, which suggested that information transfer would be severely hampered due to losing the capacity to base pair via H-bonds. Importantly, the stability of the N-glycosidic linkage, under conditions used for dry-wet cycling, was also determined. Results from this study further strengthen the hypothesis that chemical evolution in a pre-RNA World would have been vital for the evolution of informational molecules of an RNA World. This is evident in the high degree of instability displayed by N-glycosidic bonds of canonical purine ribonucleotides under the same geothermal conditions that otherwise readily favors polymerization. Significantly, the resultant product characterization in the reactions concerned underscores the difficulty associated with analyzing complex prebiotically relevant reactions due to inherent limitation of current analytical methods. Full article
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Article
Wet-Dry Cycling Delays the Gelation of Hyperbranched Polyesters: Implications to the Origin of Life
Life 2019, 9(3), 56; https://doi.org/10.3390/life9030056 - 01 Jul 2019
Cited by 9 | Viewed by 2681
Abstract
In extant biology, biopolymers perform multiple crucial functions. The biopolymers are synthesized by enzyme-controlled biosystems that would not have been available at the earliest stages of chemical evolution and consist of correctly sequenced and/or linked monomers. Some of the abiotic “messy” polymers approximate [...] Read more.
In extant biology, biopolymers perform multiple crucial functions. The biopolymers are synthesized by enzyme-controlled biosystems that would not have been available at the earliest stages of chemical evolution and consist of correctly sequenced and/or linked monomers. Some of the abiotic “messy” polymers approximate some functions of biopolymers. Condensation polymers are an attractive search target for abiotic functional polymers since principal polymers of life are produced by condensation and since condensation allows for the accurate construction of high polymers. Herein the formation of hyperbranched polyesters that have been previously used in the construction of enzyme-like catalytic complexes is explored. The experimental setup compares between the branched polyesters prepared under mild continuous heating and the wet-dry cycling associated with environmental conditions, such as dew formation or tidal activities. The results reveal that periodic wetting during which partial hydrolysis of the polyester occurs, helps to control the chain growth and delays the gel transition, a mechanism contributing to the tar formation. Moreover, the NMR and mass spec analyses indicate that continuously dried samples contain higher quantities of crosslinked and macrocyclic products, whereas cycled systems are enriched in branched structures. Ostensibly, environmental conditions have the ability to exert a rudimentary pressure to selectively enrich the polyesterification products in polymers of different structures and properties. At the early stages of chemical evolution, in the absence of biological machinery, this example of environmental control could have been for selectivity in chemical systems. As expected in marginally controlled systems, the identification of each component of the heterogeneous system has proved challenging, but it is not crucial for drawing the conclusions. Full article
(This article belongs to the Section Astrobiology)
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Perspective
Systems Analysis for Peptide Systems Chemistry
Life 2019, 9(3), 55; https://doi.org/10.3390/life9030055 - 01 Jul 2019
Cited by 1 | Viewed by 1714
Abstract
Living systems employ both covalent chemistry and physical assembly to achieve complex behaviors. The emerging field of systems chemistry, inspired by these biological systems, attempts to construct and analyze systems that are simpler than biology, while still embodying biological design principles. Due to [...] Read more.
Living systems employ both covalent chemistry and physical assembly to achieve complex behaviors. The emerging field of systems chemistry, inspired by these biological systems, attempts to construct and analyze systems that are simpler than biology, while still embodying biological design principles. Due to the multiple phenomena at play, it can be difficult to predict which phenomena will dominate and when. Conversely, there may be no single rate-limiting step, but rather a reaction network that is difficult to intuit from a purely experimental approach. Mathematical modeling can help to sort out these issues, although it can be challenging to build such models, especially for assembly kinetics. Numerical and statistical methods can play an important role to facilitate the synergistic and iterative use of modeling and experiment, and should be part of a systems chemistry curriculum. Three case studies are presented here, from our work in peptide-based systems, to illustrate some of the tools available for model construction, model simulation, and experimental design. Examples are provided in which these tools help to evaluate hypotheses, uncover design principles, and design new experiments. Full article
(This article belongs to the Special Issue Modelling Life-Like Behavior in Systems Chemistry)
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Review
State-of-the-Art Genetic Modalities to Engineer Cyanobacteria for Sustainable Biosynthesis of Biofuel and Fine-Chemicals to Meet Bio–Economy Challenges
Life 2019, 9(3), 54; https://doi.org/10.3390/life9030054 - 27 Jun 2019
Cited by 11 | Viewed by 2890
Abstract
In recent years, metabolic engineering of microorganisms has attained much research interest to produce biofuels and industrially pertinent chemicals. Owing to the relatively fast growth rate, genetic malleability, and carbon neutral production process, cyanobacteria has been recognized as a specialized microorganism with a [...] Read more.
In recent years, metabolic engineering of microorganisms has attained much research interest to produce biofuels and industrially pertinent chemicals. Owing to the relatively fast growth rate, genetic malleability, and carbon neutral production process, cyanobacteria has been recognized as a specialized microorganism with a significant biotechnological perspective. Metabolically engineering cyanobacterial strains have shown great potential for the photosynthetic production of an array of valuable native or non-native chemicals and metabolites with profound agricultural and pharmaceutical significance using CO2 as a building block. In recent years, substantial improvements in developing and introducing novel and efficient genetic tools such as genome-scale modeling, high throughput omics analyses, synthetic/system biology tools, metabolic flux analysis and clustered regularly interspaced short palindromic repeats (CRISPR)-associated nuclease (CRISPR/cas) systems have been made for engineering cyanobacterial strains. Use of these tools and technologies has led to a greater understanding of the host metabolism, as well as endogenous and heterologous carbon regulation mechanisms which consequently results in the expansion of maximum productive ability and biochemical diversity. This review summarizes recent advances in engineering cyanobacteria to produce biofuel and industrially relevant fine chemicals of high interest. Moreover, the development and applications of cutting-edge toolboxes such as the CRISPR-cas9 system, synthetic biology, high-throughput “omics”, and metabolic flux analysis to engineer cyanobacteria for large-scale cultivation are also discussed. Full article
(This article belongs to the Section Microbiology)
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