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An Inherited Efficiencies Model of Non-Genomic Evolution

A model for the evolution of biological systems in the absence of a nucleic acid-like genome is proposed and applied to model the earliest living organisms -- protocells composed of membrane encapsulated peptides. Assuming that the peptides can make and break bonds between amino acids, and bonds in non-functional peptides are more likely to be destroyed than in functional peptides, it is demonstrated that the catalytic capabilities of the system as a whole can increase. This increase is defined to be non-genomic evolution. The relationship between the proposed mechanism for evolution and recent experiments on self-replicating peptides is discussed.

New, Michael H.↗

Application of nitrogen metabolism in autotrophic bacteria to chemosynthetic bioregeneration in space missions, supplement

The chemolithotroph, Hydrogenomonas eutropha, was considered as a life support, bioregenerative system. This project focuses on several metabolic functions that are related to the proposed nitrogen cycle between man and this microbe. Specifically this organism has the capability to utilize as the sole nitrogen source such urine components as urea and fifteen individual amino acids, but not nine other amino acids. The effectiveness of utilization was high for many amino acids. Several specific growth inhibitions were also observed. The enzyme that catalyzes the incorporation of ammonia in the medium into amino acids was identified as a NADP-specific, L-glutamate dehydrogenase. This enzyme has a constitutive nature. This organism can synthesize all of its amino acids from carbon dioxide and ammonia. Therefore with the background literature of multiple pathways of individual amino acid biosyntheses, our evidence to date is consistent with the Hydrogeneomonas group having the same pathway of valine-isoleucine formation as the classical E. coli.

Wixom, R. L.↗

Modeling the Size Distribution and Chemical Composition of Secondary Organic Aerosols during the Reactive Uptake of Isoprene-Derived Epoxydiols under Low-Humidity Condition

Reactive uptake of isoprene epoxydiols (IEPOX), which are isoprene oxidation products, onto acidic sulfate aerosols is recognized to be an important mechanism for the formation of isoprene-derived secondary organic aerosol (SOA). While a mechanistic understanding of IEPOX-SOA formation exists, several processes affecting their formation remain uncertain. Evaluating mechanistic IEPOX-SOA models with controlled laboratory experiments under longer atmospherically relevant timescales is critical. Here, we implement our latest understanding of IEPOX-SOA formation within a box model to simulate the measured reactive uptake of IEPOX on polydisperse ammonium bisulfate seed aerosols within an environmental Teflon chamber. The model is evaluated with single-particle measurements of size distribution, volume, density, and composition of aerosols due to IEPOX-SOA formation at timescales of hours. Additionally, we find that the model can simulate the growth of particles due to IEPOX multiphase chemistry, as reflected in increases of the mean particle size and volume concentrations, and a shift of number size distribution to larger sizes. The model also predicts the observed evolution of particle number mean diameter and total volume concentrations at the end of the experiment. We show that in addition to self-limiting effects of IEPOX-SOA coatings, accounting for the molar balance between inorganic and organic sulfate and mass accommodation coefficient of IEPOX are important parameters governing modeling of IEPOX-SOA formation. Thus, models which do not account for the molar sulfate balance and/or diffusion limitations within IEPOX-SOA coatings are likely to predict too high IEPOX-SOA formation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Biochemical inhibition of acid phosphatase activity in two mountain spruce forest soils

The product inhibition of the 4-Methylumbelliferyl phosphate (MUB-P) decay rate, a measure of potential acid phosphatase activity, has not been considered in most of the published kinetic studies. The aim of this study was to determine the type and strength of the product inhibition in order to better define reaction conditions at which the acid phosphatase activity assay produces unbiased results. The MUB-P decay rate was measured in the forest floor and topsoil organic horizons of two spruce forest catchments at different initial MUB-P and P-PO4 3- concentrations. Furthermore, the type and strength of the inhibition was analyzed by non-linear regression. We found that MUB-P decay was competitively inhibited by the P-PO4 3- but also by dissolved organic P. By using estimated kinetic parameters, we calculated an underestimation of potential acid phosphatase activity by up to ~20% at concentrations of added MUB-P as high as 300 µmol g-1 dry weight and an incubation time one hour due to background inorganic and organic P concentrations in range of units of µmol per gram of dry soil. We discuss approaches that can be used to minimize the underestimation and show that the previously defined recommendations might not be always sufficient to avoid the bias. Therefore, we recommend to analyze progress curves at a wide range of initial MUB-P concentrations using non-linear methods when the enzyme assay is optimized for a given soil. When changes in inorganic and/or organic P concentrations are expected, we further recommend measuring background inorganic and organic P concentrations.

59 BASIC BIOLOGICAL SCIENCES↗

Methods for determining the genetic affinity of microorganisms and viruses

Selecting which sub-sequences in a database of nucleic acid such as 16S rRNA are highly characteristic of particular groupings of bacteria, microorganisms, fungi, etc. on a substantially phylogenetic tree. Also applicable to viruses comprising viral genomic RNA or DNA. A catalogue of highly characteristic sequences identified by this method is assembled to establish the genetic identity of an unknown organism. The characteristic sequences are used to design nucleic acid hybridization probes that include the characteristic sequence or its complement, or are derived from one or more characteristic sequences. A plurality of these characteristic sequences is used in hybridization to determine the phylogenetic tree position of the organism(s) in a sample. Those target organisms represented in the original sequence database and sufficient characteristic sequences can identify to the species or subspecies level. Oligonucleotide arrays of many probes are especially preferred. A hybridization signal can comprise fluorescence, chemiluminescence, or isotopic labeling, etc.; or sequences in a sample can be detected by direct means, e.g. mass spectrometry. The method's characteristic sequences can also be used to design specific PCR primers. The method uniquely identifies the phylogenetic affinity of an unknown organism without requiring prior knowledge of what is present in the sample. Even if the organism has not been previously encountered, the method still provides useful information about which phylogenetic tree bifurcation nodes encompass the organism.

Fox, George E.↗

Solid film lubricants and thermal control coatings flown aboard the EOIM-3 MDA sub-experiment

Additional experimental data were desired to support the selection of candidate thermal control coatings and solid film lubricants for the McDonnell Douglas Aerospace (MDA) Space Station hardware. The third Evaluation of Oxygen Interactions With Materials Mission (EOIM-3) flight experiment presented an opportunity to study the effects of the low Earth orbit environment on thermal control coatings and solid film lubricants. MDA provided five solid film lubricants and two anodic thermal control coatings for EOIM-3. The lubricant sample set consisted of three solid film lubricants with organic binders one solid film lubricant with an inorganic binder, and one solid film lubricant with no binder. The anodize coating sample set consisted of undyed sulfuric acid anodize and cobalt sulfide dyed sulfuric acid anodize, each on two different substrate aluminum alloys. The organic and inorganic binders in the solid film lubricants experienced erosion, and the lubricating pigments experienced oxidation. MDA is continuing to assess the effect of exposure to the low Earth orbit environment on the life and friction properties of the lubricants. Results to date support the design practice of shielding solid film lubricants from the low Earth orbit environment. Post-flight optical property analysis of the anodized specimens indicated that there were limited contamination effects and some atomic oxygen and ultraviolet radiation effects. These effects appeared to be within the values predicted by simulated ground testing and analysis of these materials, and they were different for each coating and substrate.

Murphy, Taylor J.↗

A Survey of Large Molecules toward the Protoplanetary Nebula CRL 61 8

We present the results of our survey toward the protoplanetary nebula CRL 618 for several large, highly saturated, oxygen bearing organic molecules of biological importance including acetaldehyde (CH3CHO), acetic acid (CH3OOH), dimethyl ether (CH3OCH3), ethanol (CH3CH2OH), formic acid (HCOOH) and methyl formate (HCOOCH3); large carbon chain molecules including methyl cyanide (CH3CN) , methylcyanoacetylene (CH3C3N), cyanoacetylene (HC3N), cyanodiacetylene (HC5N), and C6H; and finally smaller molecules including SO-34, SO2, O(C-34)S and MgNC. No biologically important organic molecules were detected. However, we report the first interferometric detections of CH3CN and vibrationally excited HC3N and HC5N toward this source. The temperature and distribution of CH3CN toward CRL 618 indicates it is formed in the outer envelope surrounding the UC HII region. Furthermore, the P-Cygni line profile and corresponding channel maps of vibrationally excited HC5N supports its distribution in the extended envelope expanding radially from the central star. The detection of vibrationally excited HC3N confirmed the temperature structure and column density of HC3N in the inner envelope found by Wyrowski and colleagues (2003). Finally, our observations clearly indicate that CRL 618 is a good source of large carbon chain species but is a very poor source to detect or produce organic species of biological importance.

Remijan, Anthony J.↗

Informational biopolymer structure in early living forms.

Some studies devoted to the search in various organisms for 'relics' of the biochemical nature of ancient organisms, preserved by the conservative nature of the evolutionary process in all living species, are reviewed. Investigations of five families of informational molecules constituting such 'relics' in very diverse organisms are reported. They include: cytochrome c, ferredoxin, trypsin, transfer ribonucleic acid (RNA), and 5S ribosomal RNA. It is shown that, even from these few informational molecules, some interesting inferences about early living organisms can be drawn.

Dayhoff, M. O.↗

The potential role of organics in new particle formation and initial growth in the remote tropical upper troposphere

Abstract. Global observations and model studies indicate that new particle formation (NPF) in the upper troposphere (UT) and subsequent particles supply 40 %–60 % of cloud condensation nuclei (CCN) in the lower troposphere, thus affecting the Earth's radiative budget. There are several plausible nucleation mechanisms and precursor species in this atmospheric region, which, in the absence of observational constraints, lead to uncertainties in modeled aerosols. In particular, the type of nucleation mechanism and concentrations of nucleation precursors, in part, determine the spatial distribution of new particles and resulting spatial distribution of CCN from this source. Although substantial advances in understanding NPF have been made in recent years, NPF processes in the UT in pristine marine regions are still poorly understood and are inadequately represented in global models. Here, we evaluate commonly used and state-of-the-art NPF schemes in a Lagrangian box model to assess which schemes and precursor concentrations best reproduce detailed in situ observations. Using measurements of aerosol size distributions (0.003 < Dp < 4.8 µm) in the remote marine troposphere between ∼0.18 and 13 km altitude obtained during the NASA Atmospheric Tomography (ATom) mission, we show that high concentrations of newly formed particles in the tropical UT over both the Atlantic and Pacific oceans are associated with outflow regions of deep convective clouds. We focus analysis on observations over the remote Pacific Ocean, which is a region less perturbed by continental emissions than the Atlantic. Comparing aerosol size distribution measurements over the remote Pacific with box model simulations for 32 cases shows that none of the NPF schemes most commonly used in global models, including binary nucleation of sulfuric acid and water (neutral and ion-assisted) and ternary involving sulfuric acid, water, and ammonia, are consistent with observations, regardless of precursor concentrations. Through sensitivity studies, we find that the nucleation scheme among those tested that is able to explain most consistently (21 of 32 cases) the observed size distributions is that of Riccobono et al. (2014), which involves both organic species and sulfuric acid. The method of Dunne et al. (2016), involving charged sulfuric acid–water–ammonia nucleation, when coupled with organic growth of the nucleated particles, was most consistent with the observations for 5 of 32 cases. Similarly, the neutral sulfuric acid–water–ammonia method of Napari (2002), when scaled with a tuning factor and with organic growth added, was most consistent for 6 of 32 cases. We find that to best reproduce both nucleation and growth rates, the mixing ratios of gas-phase organic precursors generally need to be at least twice that of SO2, a proxy for dimethyl sulfide (DMS). Unfortunately, we have no information on the nature of oxidized organic species that participated in NPF in this region. Global models rarely include organic-driven nucleation and growth pathways in UT conditions where globally significant NPF takes place, which may result in poor estimates of NPF and CCN abundance and contribute to uncertainties in aerosol–cloud–radiation effects. Furthermore, our results indicate that the organic aerosol precursor vapors may be important in the tropical UT above marine regions, a finding that should guide future observational efforts.

54 ENVIRONMENTAL SCIENCES↗

Amino acids in a carbonaceous chondrite from Antarctica

A carbonaceous chondrite from the Antarctic, referred to as the Allan Hills meteorite 77306, appears to be free from terrestrial organic contamination. The presence of both protein and non-protein amino acids and an equal abundance of D- and L-enantiomers of amino acids, is testimony to the extraterrestrial nature of these compounds.

Kotra, R. K.↗

Unnatural selection in chemical systems

The theory of evolution through natural selection was proposed by Darwin and Wallace to explain how the characteristics of populations of animals change with time. An examination of their assumptions shows that the theory has much broader application than they originally envisaged. We now know that in appropriate environments RNA molecules or computer viruses, for example, can evolve. The adventure with which we are concerned is the quest for chemical systems that undergo processes analogous to Darwinian selection in the test tube. The search is not restricted to systems that are closely related to nucleic acids, although most of the available experimental evidence concerns such systems. A population of molecules satisfies all the requirements of the theory is there are different kinds of molecules in the population and if each individual molecule can direct the formation of copies of itself, then a population of molecules will adapt to a varying environment by changing its composition so as to maintain as high as possible a rate of replication. Sol Spiegelman is the inventor of 'unnatural selection'. He showed clearly that populations of RNA molecules evolve when replicated repeatedly by Q beta RNA polymerase under a chosen set of adverse reaction conditions. In the systems that he studied, the initial population was fairly homogeneous and much of the variation was created during the course of the experiment by mutation, that is, error of replication. The term 'unnatural selection' will be used loosely to describe evolution of nucleic acids or other replicatable polymers in vitro. The term 'Natural Selection' will be reserved for the evolution of living organisms and their viruses. Natural Section usually involves the coevolution of nucleic acids and proteins, while 'unnatural selection', as practiced so far, allows replicating nucleic acids to evolve but hold constant the enzymes that catalyze replication. It is widely believed that biology based on DNA, RNA, and proteins was preceded by the biology of an 'RNA world' in which enzymes were composed of RNA alone. The origin of RNA replication is thus the central puzzle of the origins of life. Consequently, RNA-catalyzed RNA replication is presently one of the main goals of experimental work on unnatural selection. However, there is also a more distant goal, namely, to achieve replication and selection in systems unrelated to RNA. These different systems are discussed in this article.

Orgel, Leslie E.↗

Strategies for Distinguishing Abiotic Chemistry from Martian Biochemistry in Samples Returned from Mars

A key goal in the search for evidence of extinct or extant life on Mars will be the identification of chemical biosignatures including complex organic molecules common to all life on Earth. These include amino acids, the monomer building blocks of proteins and enzymes, and nucleobases, which serve as the structural basis of information storage in DNA and RNA. However, many of these organic compounds can also be formed abiotically as demonstrated by their prevalence in carbonaceous meteorites [1]. Therefore, an important challenge in the search for evidence of life on Mars will be distinguishing between abiotic chemistry of either meteoritic or martian origin from any chemical biosignatures from an extinct or extant martian biota. Although current robotic missions to Mars, including the 2011 Mars Science Laboratory (MSL) and the planned 2018 ExoMars rovers, will have the analytical capability needed to identify these key classes of organic molecules if present [2,3], return of a diverse suite of martian samples to Earth would allow for much more intensive laboratory studies using a broad array of extraction protocols and state-of-theart analytical techniques for bulk and spatially resolved characterization, molecular detection, and isotopic and enantiomeric compositions that may be required for unambiguous confirmation of martian life. Here we will describe current state-of-the-art laboratory analytical techniques that have been used to characterize the abundance and distribution of amino acids and nucleobases in meteorites, Apollo samples, and comet- exposed materials returned by the Stardust mission with an emphasis on their molecular characteristics that can be used to distinguish abiotic chemistry from biochemistry as we know it. The study of organic compounds in carbonaceous meteorites is highly relevant to Mars sample return analysis, since exogenous organic matter should have accumulated in the martian regolith over the last several billion years and the analytical techniques previously developed for the study of extraterrestrial materials can be applied to martian samples.

Glavin, D. P.↗

Phosphorylation of Glyceric Acid in Aqueous Solution Using Trimetaphosphate

The phosphorylation of glyceric acid is an interesting prebiotic reaction because it converts a simple, potentially prebiotic organic molecule into phosphate derivatives that are central to carbohydrate metabolism. We find that 0.05 M glyceric acid in the presence of 0.5 M trimetaphosphate in alkaline solution gives a mixture of 2- and 3-phosphoglyceric acids in combined yields of up to 40%.

Kolb, Vera↗

Flexible polyurethanes, renewable fuels, and flavorings from a microalgae oil waste stream

Renewable polymers have become an important focus in next-generation materials, and algae biomass offers an environmentally low-impact feedstock that can serve multiple uses. This study aims to develop a scalable methodology for production of microalgae-based polyols for polyurethane synthesis from waste oils derived from algae biomass. Following separation of omega-3 fatty acids from algae oil, residual oils can offer valuable building blocks for petrochemical replacements. However, unlike vegetable oils, algae oils contain organic contaminants, including photosynthetic pigments and hydrophobic cofactors that can complicate preparative methodologies. Here we convert and purify waste streams from omega-3 depleted Nannochloropsis salina algae oil, with major components consisting of palmitic and palmitoleic acid, into azelaic acid (AA) as a building block for flexible polyurethanes, with a simultaneous production of heptanoic acid (HA) as a flavor and fragrance precursor. Conversion of free fatty acid mixtures into a soft soap allows extraction of organic contaminants, and urea complexation provides isolated palmitoleic acid, which is subsequently ozonolyzed to produce AA and HA. Bio-based polyester diols are prepared from AA via esterification to provide a polyol monomer for flexible polyurethane foam preparation. The HA co-product is modified to produce the flavoring agent methyl heptanoate and also decarboxylated to produce hexane as a renewable solvent. This scalable process can be performed on oils from multiple algal species, offering valuable monomers from a highly sustainable source.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Search for Sugars and Related Compounds in Residues Produced from the UV Irradiation of Astrophysical Ice Analogs

A large variety and number of organic compounds of prebiotic interest have been detected in meteorites. Among them, one sugar (dihydroxyacetone) as well as several sugar acids and sugar alcohols have been detected in Murchison and Murray [1]. Their presence in meteorites, along with amino acids, amphiphiles, and nucleobases [2-6], strongly suggests that molecules essential to life can form abiotically under astrophysical conditions. This hypothesis is supported by laboratory studies on the formation of complex organic molecules from the ultraviolet (UV) irradiation of astrophysical ice analogs (H2O, CO, CO2, CH3OH, CH4, NH3, etc.). These studies show that the organic residues recovered at room temperature after the UV irradiation of such ice mixtures contain amino acids [7-9], amphiphiles [4], nucleobases [10-13], and other organic complex organic compounds [14-16]. However, no systematic search for the presence of sugars, sugar acids, and sugar alcohols in laboratory residues have been reported to date, despite the fact that those compounds are involved in a large number of biological processes. Only a limited number of small (less than or equal to 3 carbon atoms) sugar derivatives such as glycerol and glyceric acid have been detected in residues [14-16]. In this work, we show results obtained from the systematic search for sugars and sugar-related compounds in organic residues produced from the UV irradiation of simple CH3OH and H2O+CH3OH ices, and more astrophysically relevant ice mixtures containing H2O, CH3OH, CO, and NH3. The results are compared with measurements of sugars and related compounds in primitive meteorites.

Murchison and Murray↗

The role of Ca-bridged organic matter in an alkaline soil, as revealed by multimodal chemical imaging

Mineral–organic matter (OM) studies have predominantly focused on acidic soils that are abundant in iron (Fe) oxides and aluminum (Al) oxides. We have probed mineral–OM interactions in an alkaline or calcareous soil of the Aridisols class. Unlike the role of Fe and Al, the role of Ca-minerals (particularly calcite), which are ubiquitous in alkaline soils, in OM sequestration is not well understood. Multiple recent model studies with aqueous Ca2+ or synthetic calcite and a suite of OM compounds have shown Ca-OM assemblages to be spatially correlated with calcite at the microscale. To study the chemical state of both Ca and Fe and their competing role in soil organic matter (SOM) stabilization, we performed laboratory characterization using x-ray diffraction, Mössbauer spectroscopy, x-ray photoelectron spectroscopy, scanning electron microscopy, and scanning transmission electron microscopy, alongside synchrotron-based microscale chemical imaging using scanning transmission x-ray microscopy combined with near-edge x-ray absorption fine structure. Ca mineral–organic associations were found to be ubiquitous in this system and are likely critical for understanding SOM stabilization/degradation in alkaline soils. From our findings on mineralogy, speciation, and the nature of Ca-OM bridging, we identified differences in C and Ca chemistry based on the relative location of OM to Ca minerals. The OM near the calcite crystal was enriched in lipid and protein moieties, Ca-OM next to Fe minerals displayed a strong contribution from aromatic compounds, while on the surface of microbes, the carbonate was believed to be of microbial in origin, as also suggested by preliminary works reporting on the formation of amorphous calcite or nano-calcite. In Ca-OM admixed with carbonate, it was difficult to distinguish Ca-associated OM from amorphous calcite or nano-calcite.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Critical fluctuations in liquid–liquid extraction organic phases controlled by extractant and diluent molecular structure

Extractant aggregation in liquid–liquid extraction organic phases impacts extraction energetics and is related to the deleterious efficiency-limiting liquid–liquid phase transition known as third phase formation. Using small angle X-ray scattering, we find that structural heterogeneities across a wide range of compositions in binary mixtures of malonamide extractants and alkane diluents are well described by Ornstein–Zernike scattering. This suggests that structure in these simplified organic phases originates from the critical point associated with the liquid–liquid phase transition. To confirm this, we measure the temperature dependence of the organic phase structure, finding critical exponents consistent with the 3D Ising model. Molecular dynamics simulations were also consistent with this mechanism for extractant aggregation. Due to the absence of water or any other polar solutes required to form reverse-micellar-like nanostructures, these fluctuations are inherent to the binary extractant/diluent mixture. Further, we also show how the molecular structure of the extractant and diluent modulate these critical concentration fluctuations by shifting the critical temperature: critical fluctuations are suppressed by increasing extractant alkyl tail lengths or decreasing diluent alkyl chain lengths. This is consistent with how extractant and diluent molecular structure are known to impact metal and acid loading capacity in many-component LLE organic phases, suggesting phase behavior of practical systems may be effectively studied in simplified organic phases. Overall, the explicit connection between molecular structure, aggregation and phase behavior demonstrated here will enable the design of more efficient separations processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Adaptive Laboratory Evolution for Enhanced Performance of Cupriavidus necator on Formic Acid

The need to decarbonize our economy is becoming ever more pressing. CO2, can be electrochemically reduced to formic acid, a soluble C1 molecule that can be used to store carbon and energy. Cupriavidus necator H16, a soil bacterium, capable of consuming and growing on formic acid as its sole carbon source, is well positioned to upgrade CO2-derived formic acid into value added chemicals such as sustainable aviation fuel. To improve the performance of C. necator on formic acid adaptive laboratory evolution (ALE), a proven tool for improving microbial fitness, has been conducted using continuous pH-stat bioreactors. The system works on the basis that consumption of formic acid raises the pH and triggers the addition of more formic acid to maintain the pH at 6.7, such that formic acid is provided at the same rate as it is consumed. This system has been coupled with level control to achieve continuous fermentation where cells acquiring mutations that improve growth on formic acid become more abundant in the population, from which they can be isolate and characterized. This configuration where the dilution rate is controlled by pH-stat has been found to seek out a dilution rate that matches the exponential growth rate of the organism. During developmental experiments it was discovered that formic acid accumulated to inhibitory levels. It was determined that the nitrogen source, ammonium hydroxide, must be tailored to the carbon consumption to avoid formic acid accumulation. ALE has run in three lineages for 2000+ hours and 300+ generations. Growth of evolved isolates derived from all lineages will be evaluated on formic acid and those with improved growth rates or biomass yield will be subjected to whole genome sequencing to identify potentially causative mutations. These mutations will be evaluated individually and in combination to identify those that improve growth on formic acid.

adaptive laboratory evolution↗