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Volume 9, September

Life, Volume 9, Issue 4 (December 2019) – 10 articles

Cover Story (view full-size image): To be accepted as "prebiotic", the process of making RNA must be simple. However, RNA seems intrinsically complicated, as are most proposals for its formation, involving multi-step sequences that need human intervention to manage self-reacting intermediates, orchestrate reagent addition, and schedule photon irradiation. However, some prebiotic chemistry is inevitable. Formaldehyde and trace glycolaldehyde almost certainly formed and reacted with volcanic SO2 to give semi-stable products. Rained into borate-containing aquifers, these products produced 5-carbon sugars like ribose. Mid-sized impacts intermittently created hazy atmospheres that delivered nucleobase precursors to those aquifers. With drying, mineral-organic interactions assemble phosphorylated nucleosides and oligomeric RNA from these. These chemistries suggest that RNA is an intrinsic outcome of simple chemistry on rocky planets. View this [...] Read more.
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Article
Survivability of Anhydrobiotic Cyanobacteria in Salty Ice: Implications for the Habitability of Icy Worlds
Life 2019, 9(4), 86; https://doi.org/10.3390/life9040086 - 22 Nov 2019
Cited by 4 | Viewed by 1860
Abstract
Two anhydrobiotic strains of the cyanobacterium Chroococcidiopsis, namely CCMEE 029 and CCMEE 171, isolated from the Negev Desert in Israel and from the Dry Valleys in Antarctica, were exposed to salty-ice simulations. The aim of the experiment was to investigate the cyanobacterial [...] Read more.
Two anhydrobiotic strains of the cyanobacterium Chroococcidiopsis, namely CCMEE 029 and CCMEE 171, isolated from the Negev Desert in Israel and from the Dry Valleys in Antarctica, were exposed to salty-ice simulations. The aim of the experiment was to investigate the cyanobacterial capability to survive under sub-freezing temperatures in samples simulating the environment of icy worlds. The two strains were mixed with liquid solutions having sub-eutectic concentration of Na2SO4, MgSO4 and NaCl, then frozen down to different final temperatures (258 K, 233 K and 203 K) in various experimental runs. Both strains survived the exposure to 258 K in NaCl solution, probably as they migrated in the liquid veins between ice grain boundaries. However, they also survived at 258 K in Na2SO4 and MgSO4-salty-ice samples—that is, a temperature well below the eutectic temperature of the solutions, where liquid veins should not exist anymore. Moreover, both strains survived the exposure at 233 K in each salty-ice sample, with CCMEE 171 showing an enhanced survivability, whereas there were no survivors at 203 K. The survival limit at low temperature was further extended when both strains were exposed to 193 K as air-dried cells. The results suggest that vitrification might be a strategy for microbial life forms to survive in potentially habitable icy moons, for example in Europa’s icy crust. By entering a dried, frozen state, they could be transported from niches, which became non-habitable to new habitable ones, and possibly return to metabolic activity. Full article
(This article belongs to the Special Issue Planetary Exploration of Habitable Environments)
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Article
Membrane Lipid Composition and Amino Acid Excretion Patterns of Methanothermococcus okinawensis Grown in the Presence of Inhibitors Detected in the Enceladian Plume
Life 2019, 9(4), 85; https://doi.org/10.3390/life9040085 - 14 Nov 2019
Cited by 7 | Viewed by 1717
Abstract
Lipids and amino acids are regarded as important biomarkers for the search for extraterrestrial life in the Solar System. Such biomarkers may be used to trace methanogenic life on other planets or moons in the Solar System, such as Saturn’s icy moon Enceladus. [...] Read more.
Lipids and amino acids are regarded as important biomarkers for the search for extraterrestrial life in the Solar System. Such biomarkers may be used to trace methanogenic life on other planets or moons in the Solar System, such as Saturn’s icy moon Enceladus. However, little is known about the environmental conditions shaping the synthesis of lipids and amino acids. Here, we present the lipid production and amino acid excretion patterns of the methanogenic archaeon Methanothermococcus okinawensis after exposing it to different multivariate concentrations of the inhibitors ammonium, formaldehyde, and methanol present in the Enceladian plume. M. okinawensis shows different patterns of lipid and amino acids excretion, depending on the amount of these inhibitors in the growth medium. While methanol did not show a significant impact on growth, lipid or amino acid production rates, ammonium and formaldehyde strongly affected these parameters. These findings are important for understanding the eco-physiology of methanogens on Earth and have implications for the use of biomarkers as possible signs of extraterrestrial life for future space missions in the Solar System. Full article
(This article belongs to the Section Astrobiology)
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Article
Prebiotic Chemistry that Could Not Not Have Happened
Life 2019, 9(4), 84; https://doi.org/10.3390/life9040084 - 14 Nov 2019
Cited by 15 | Viewed by 2602
Abstract
We present a direct route by which RNA might have emerged in the Hadean from a fayalite–magnetite mantle, volcanic SO2 gas, and well-accepted processes that must have created substantial amounts of HCHO and catalytic amounts of glycolaldehyde in the Hadean atmosphere. In [...] Read more.
We present a direct route by which RNA might have emerged in the Hadean from a fayalite–magnetite mantle, volcanic SO2 gas, and well-accepted processes that must have created substantial amounts of HCHO and catalytic amounts of glycolaldehyde in the Hadean atmosphere. In chemistry that could not not have happened, these would have generated stable bisulfite addition products that must have rained to the surface, where they unavoidably would have slowly released reactive species that generated higher carbohydrates. The formation of higher carbohydrates is self-limited by bisulfite formation, while borate minerals may have controlled aldol reactions that occurred on any semi-arid surface to capture that precipitation. All of these processes have well-studied laboratory correlates. Further, any semi-arid land with phosphate should have had phosphate anhydrides that, with NH3, gave carbohydrate derivatives that directly react with nucleobases to form the canonical nucleosides. These are phosphorylated by magnesium borophosphate minerals (e.g., lüneburgite) and/or trimetaphosphate-borate with Ni2+ catalysis to give nucleoside 5′-diphosphates, which oligomerize to RNA via a variety of mechanisms. The reduced precursors that are required to form the nucleobases came, in this path-hypothesis, from one or more mid-sized (1023–1020 kg) impactors that almost certainly arrived after the Moon-forming event. Their iron metal content almost certainly generated ammonia, nucleobase precursors, and other reduced species in the Hadean atmosphere after it transiently placed the atmosphere out of redox equilibrium with the mantle. In addition to the inevitability of steps in this path-hypothesis on a Hadean Earth if it had semi-arid land, these processes may also have occurred on Mars. Adapted from a lecture by the Corresponding Author at the All-Russia Science Festival at the Lomonosov Moscow State University on 12 October 2019, and is an outcome of a three year project supported by the John Templeton Foundation and the NASA Astrobiology program. Dedicated to David Deamer, on the occasion of his 80th Birthday. Full article
(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)
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Review
Lipid-Assisted Polymerization of Nucleotides
Life 2019, 9(4), 83; https://doi.org/10.3390/life9040083 - 05 Nov 2019
Cited by 1 | Viewed by 1800
Abstract
In addition to being one of the proponents of the “Lipid World hypothesis”, David Deamer, together with other colleagues, pioneered studies involving formation of RNA-like oligomers from their ‘non-activated’, prebiotically plausible monomeric moieties. In particular, the pioneering work in this regard was a [...] Read more.
In addition to being one of the proponents of the “Lipid World hypothesis”, David Deamer, together with other colleagues, pioneered studies involving formation of RNA-like oligomers from their ‘non-activated’, prebiotically plausible monomeric moieties. In particular, the pioneering work in this regard was a publication from 2008 in Origins of Life and Evolution of Biospheres, The Journal of the International Astrobiology Society, wherein we described the formation of RNA-like oligomers from nucleoside 5’-monophosphates. In that study, we had simulated a terrestrial geothermal environment, a niche that is thought to have facilitated the prebiotic non-enzymatic synthesis of polynucleotides. We showed that a mixture of lipids and non-activated mononucleotides resulted in the formation of relatively long strands of RNA-like polymers when subjected to repeated cycles of dehydration and rehydration (DH-RH). Since 2008, terrestrial geothermal niches and DH-RH conditions have been explored in the context of several other prebiotic processes. In this article, we review the work that we and other researchers have carried out since then in this line of research, including the development of new apparatus to carry out the simulation of prebiotic terrestrial geothermal environments. Full article
(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)
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Article
Detection of Biological Bricks in Space. The Case of Adenine in Silica Aerogel
Life 2019, 9(4), 82; https://doi.org/10.3390/life9040082 - 26 Oct 2019
Viewed by 1796
Abstract
Space missions using probes to return dust samples are becoming more frequent. Dust collectors made of silica aerogel blocks are used to trap and bring back extraterrestrial particles for analysis. In this work, we show that it is possible to detect traces of [...] Read more.
Space missions using probes to return dust samples are becoming more frequent. Dust collectors made of silica aerogel blocks are used to trap and bring back extraterrestrial particles for analysis. In this work, we show that it is possible to detect traces of adenine using surface-enhanced Raman spectroscopy (SERS). The method was first optimized using adenine deposition on glass slides and in glass wells. After this preliminary step, adenine solution was injected into the silica aerogel. Finally, gaseous adenine was successfully trapped in the aerogel. The presence of traces of adenine was monitored by SERS through its characteristic bands at 732, 1323, and 1458 cm−1 after the addition of the silver Creighton colloid. Such a method can be extended in the frame of Tanpopo missions for studying the interplanetary transfer of prebiotic organic compounds of biological interest. Full article
(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)
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Article
Wheat Space Odyssey: “From Seed to Seed”. Kernel Morphology
Life 2019, 9(4), 81; https://doi.org/10.3390/life9040081 - 25 Oct 2019
Cited by 4 | Viewed by 2017
Abstract
The long-term autonomous existence of man in extraterrestrial conditions is associated with the need to cultivate plants—the only affordable and effective means for both providing oxygen and CO2 utilization, and providing one of the most habitual and energetically valuable products: plant food. [...] Read more.
The long-term autonomous existence of man in extraterrestrial conditions is associated with the need to cultivate plants—the only affordable and effective means for both providing oxygen and CO2 utilization, and providing one of the most habitual and energetically valuable products: plant food. In this study, we analyzed the results of the space odyssey of wheat and compared the morphological features of parental grains harvested from soil grown wheat plants, the grains obtained from plants grown in a specialized device for plant cultivation—the “Lada” space greenhouses during space flight in the ISS, and the grains obtained from plants in the same device on Earth. The seeds obtained under various conditions were studied using scanning electron microscopy. We studied the mutual location of the surface layers of the kernel cover tissues, the structural features of the tube and cross cells of the fruit coat (pericarp), and the birsh hairs of the kernels. It was found that the grains obtained under wheat plants cultivation on board of the ISS in near space had some specific differences from the parental, original grains, and the grains obtained from plants grown in the “Lada” greenhouse in ground conditions. These changes were manifested in a shortening of the birsh hairs, and a change in the size and relative arrangement of the cells of the kernel coat. We suggest that such changes are a manifestation of the sensitivity of the cytoskeleton reorganization systems and water exchange to the influence of particular physical conditions of space flight (microgravity, increased doses of radiation, etc.). Thus, the revealed changes did not hinder the wheat grains production “from seed to seed”, which allows the cultivation of this crop in stable life support systems in near earth orbit. Full article
(This article belongs to the Special Issue Space Experiments for Astrobiology)
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Article
Chemical Ecosystem Selection on Mineral Surfaces Reveals Long-Term Dynamics Consistent with the Spontaneous Emergence of Mutual Catalysis
Life 2019, 9(4), 80; https://doi.org/10.3390/life9040080 - 23 Oct 2019
Cited by 13 | Viewed by 6074
Abstract
How did chemicals first become organized into systems capable of self-propagation and adaptive evolution? One possibility is that the first evolvers were chemical ecosystems localized on mineral surfaces and composed of sets of molecular species that could catalyze each other’s formation. We used [...] Read more.
How did chemicals first become organized into systems capable of self-propagation and adaptive evolution? One possibility is that the first evolvers were chemical ecosystems localized on mineral surfaces and composed of sets of molecular species that could catalyze each other’s formation. We used a bottom-up experimental framework, chemical ecosystem selection (CES), to evaluate this perspective and search for surface-associated and mutually catalytic chemical systems based on the changes in chemistry that they are expected to induce. Here, we report the results of preliminary CES experiments conducted using a synthetic “prebiotic soup” and pyrite grains, which yielded dynamical patterns that are suggestive of the emergence of mutual catalysis. While more research is needed to better understand the specific patterns observed here and determine whether they are reflective of self-propagation, these results illustrate the potential power of CES to test competing hypotheses for the emergence of protobiological chemical systems. Full article
(This article belongs to the Special Issue Systems Protobiology: Origin of Life by Mutually Catalytic Networks)
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Article
Nitrates as a Potential N Supply for Microbial Ecosystems in a Hyperarid Mars Analog System
Life 2019, 9(4), 79; https://doi.org/10.3390/life9040079 - 19 Oct 2019
Cited by 6 | Viewed by 1891
Abstract
Nitrate is common in Mars sediments owing to long-term atmospheric photolysis, oxidation, and potentially, impact shock heating. The Atacama Desert in Chile, which is the driest region on Earth and rich in nitrate deposits, is used as a Mars analog in this study [...] Read more.
Nitrate is common in Mars sediments owing to long-term atmospheric photolysis, oxidation, and potentially, impact shock heating. The Atacama Desert in Chile, which is the driest region on Earth and rich in nitrate deposits, is used as a Mars analog in this study to explore the potential effects of high nitrate levels on growth of extremophilic ecosystems. Seven study sites sampled across an aridity gradient in the Atacama Desert were categorized into 3 clusters—hyperarid, middle, and arid sites—as defined by essential soil physical and chemical properties. Intriguingly, the distribution of nitrate concentrations in the shallow subsurface suggests that the buildup of nitrate is not solely controlled by precipitation. Correlations of nitrate with SiO2/Al2O3 and grain sizes suggest that sedimentation rates may also be important in controlling nitrate distribution. At arid sites receiving more than 10 mm/yr precipitation, rainfall shows a stronger impact on biomass than nitrate does. However, high nitrate to organic carbon ratios are generally beneficial to N assimilation, as evidenced both by soil geochemistry and enriched culturing experiments. This study suggests that even in the absence of precipitation, nitrate levels on a more recent, hyperarid Mars could be sufficiently high to benefit potentially extant Martian microorganisms. Full article
(This article belongs to the Special Issue Selected Papers from 8th Astrobiology Society of Britain Conference)
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Article
Survival of Self-Replicating Molecules under Transient Compartmentalization with Natural Selection
Life 2019, 9(4), 78; https://doi.org/10.3390/life9040078 - 03 Oct 2019
Cited by 2 | Viewed by 1824
Abstract
The problem of the emergence and survival of self-replicating molecules in origin-of-life scenarios is plagued by the error catastrophe, which is usually escaped by considering effects of compartmentalization, as in the stochastic corrector model. By addressing the problem in a simple system composed [...] Read more.
The problem of the emergence and survival of self-replicating molecules in origin-of-life scenarios is plagued by the error catastrophe, which is usually escaped by considering effects of compartmentalization, as in the stochastic corrector model. By addressing the problem in a simple system composed of a self-replicating molecule (a replicase) and a parasite molecule that needs the replicase for copying itself, we show that transient (rather than permanent) compartmentalization is sufficient to the task. We also exhibit a regime in which the concentrations of the two kinds of molecules undergo sustained oscillations. Our model should be relevant not only for origin-of-life scenarios but also for describing directed evolution experiments, which increasingly rely on transient compartmentalization with pooling and natural selection. Full article
(This article belongs to the Section Origin of Life)
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Review
Twenty Years of “Lipid World”: A Fertile Partnership with David Deamer
Life 2019, 9(4), 77; https://doi.org/10.3390/life9040077 - 20 Sep 2019
Cited by 4 | Viewed by 2064
Abstract
“The Lipid World” was published in 2001, stemming from a highly effective collaboration with David Deamer during a sabbatical year 20 years ago at the Weizmann Institute of Science in Israel. The present review paper highlights the benefits of this scientific interaction and [...] Read more.
“The Lipid World” was published in 2001, stemming from a highly effective collaboration with David Deamer during a sabbatical year 20 years ago at the Weizmann Institute of Science in Israel. The present review paper highlights the benefits of this scientific interaction and assesses the impact of the lipid world paper on the present understanding of the possible roles of amphiphiles and their assemblies in the origin of life. The lipid world is defined as a putative stage in the progression towards life’s origin, during which diverse amphiphiles or other spontaneously aggregating small molecules could have concurrently played multiple key roles, including compartment formation, the appearance of mutually catalytic networks, molecular information processing, and the rise of collective self-reproduction and compositional inheritance. This review brings back into a broader perspective some key points originally made in the lipid world paper, stressing the distinction between the widely accepted role of lipids in forming compartments and their expanded capacities as delineated above. In the light of recent advancements, we discussed the topical relevance of the lipid worldview as an alternative to broadly accepted scenarios, and the need for further experimental and computer-based validation of the feasibility and implications of the individual attributes of this point of view. Finally, we point to possible avenues for exploring transition paths from small molecule-based noncovalent structures to more complex biopolymer-containing proto-cellular systems. Full article
(This article belongs to the Special Issue Themed Issue Commemorating Prof. David Deamer's 80th Birthday)
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