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Life, Volume 9, Issue 3 (September 2019)

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Open AccessArticle
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
Received: 16 June 2019 / Revised: 8 July 2019 / Accepted: 12 July 2019 / Published: 14 July 2019
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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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Open AccessEssay
The Essence of Systems Chemistry
Received: 18 April 2019 / Revised: 6 June 2019 / Accepted: 25 June 2019 / Published: 11 July 2019
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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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Open AccessReview
Synthetic Approaches for Nucleic Acid Delivery: Choosing the Right Carriers
Received: 24 May 2019 / Revised: 2 July 2019 / Accepted: 3 July 2019 / Published: 9 July 2019
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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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Open AccessConcept Paper
The Role of Orthogonality in Genetic Code Expansion
Received: 20 June 2019 / Revised: 1 July 2019 / Accepted: 1 July 2019 / Published: 5 July 2019
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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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Open AccessArticle
Formation of Abasic Oligomers in Nonenzymatic Polymerization of Canonical Nucleotides
Received: 31 May 2019 / Revised: 30 June 2019 / Accepted: 1 July 2019 / Published: 4 July 2019
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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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Open AccessArticle
Wet-Dry Cycling Delays the Gelation of Hyperbranched Polyesters: Implications to the Origin of Life
Received: 7 May 2019 / Revised: 11 June 2019 / Accepted: 28 June 2019 / Published: 1 July 2019
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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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Open AccessPerspective
Systems Analysis for Peptide Systems Chemistry
Received: 13 April 2019 / Revised: 14 June 2019 / Accepted: 25 June 2019 / Published: 1 July 2019
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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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Open AccessReview
State-of-the-Art Genetic Modalities to Engineer Cyanobacteria for Sustainable Biosynthesis of Biofuel and Fine-Chemicals to Meet Bio–Economy Challenges
Received: 22 April 2019 / Revised: 15 June 2019 / Accepted: 26 June 2019 / Published: 27 June 2019
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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 Life Sciences)
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