Chemomicrobiome analysis of the ornithine molecule

Hepatoprotectors and prebiotic molecules that promote the growth of intestinal flora differ significantly in their effects on different representatives of the human microbiome. This work presents the results of a comparative chemomicrobiomic analysis of ornithine and reference molecules (S-ademetionine, ursodeoxycholic acid, lactulose, and fructose). For each of the studied molecules, estimates of the values of the area under the growth curve were obtained for a representative sample of human microbiota, which included 38 commensal bacteria (including bifidobacteria and lactobacilli) and the values of the minimum inhibitory concentrations (MIC) for 152 strains of pathogenic bacteria. It has been shown that ornithine, to a lesser extent than the reference molecules, stimulates the growth of pathogenic bacteria of the genera Aspergillus, Klebsiella, Pseudomonas, Staphylococcus and Candida fungi. Ornithine is also less likely to stimulate the growth of more aggressive bacteria (Biosafety Level 2) and to a greater extent less aggressive bacteria (Biosafety Level 1). By stimulating butyric and other short-chain fatty acid-producing microorganisms, ornithine can improve the profile of gut microbiota.

The Role of Terahertz and Far-IR Spectroscopy in Understanding the Formation and Evolution of Interstellar Prebiotic Molecules

Stellar systems are often formed through the collapse of dense molecular clouds which, in turn, return copious amounts of atomic and molecular material to the interstellar medium. An in-depth understanding of chemical evolution during this cyclic interaction between the stars and the interstellar medium is at the heart of astrochemistry. Systematic chemical composition changes as interstellar clouds evolve from the diffuse stage to dense, quiescent molecular clouds to star-forming regions and proto-planetary disks further enrich the molecular diversity leading to the evolution of ever more complex molecules. In particular, the icy mantles formed on interstellar dust grains and their irradiation are thought to be the origin of many of the observed molecules, including those that are deemed to be “prebiotic”; that is those molecules necessary for the origin of life. This review will discuss both observational (e.g., ALMA, SOFIA, Herschel) and laboratory investigations using terahertz and far-IR (THz/F-IR) spectroscopy, as well as centimeter and millimeter spectroscopies, and the role that they play in contributing to our understanding of the formation of prebiotic molecules. Mid-IR spectroscopy has typically been the primary tool used in laboratory studies, particularly those concerned with interstellar ice analogues. However, THz/F-IR spectroscopy offers an additional and complementary approach in that it provides the ability to investigate intermolecular interactions compared to the intramolecular modes available in the mid-IR. THz/F-IR spectroscopy is still somewhat under-utilized, but with the additional capability it brings, its popularity is likely to significantly increase in the near future. This review will discuss the strengths and limitations of such methods, and will also provide some suggestions on future research areas that should be pursued in the coming decade exploiting both space-borne and laboratory facilities.

Thermodynamics of Potential CHO Metabolites in a Reducing Environment

How did metabolism arise and evolve? What chemical compounds might be suitable to support and sustain a proto-metabolism before the advent of more complex co-factors? We explore these questions by using first-principles quantum chemistry to calculate the free energies of CHO compounds in aqueous solution, allowing us to probe the thermodynamics of core extant cycles and their closely related chemical cousins. By framing our analysis in terms of the simplest feasible cycle and its permutations, we analyze potentially favorable thermodynamic cycles for CO2 fixation with H2 as a reductant. We find that paying attention to redox states illuminates which reactions are endergonic or exergonic. Our results highlight the role of acetate in proto-metabolic cycles, and its connection to other prebiotic molecules such as glyoxalate, glycolaldehyde, and glycolic acid.

Proliferating coacervate droplets as the missing link between chemistry and biology in the origins of life

The hypothesis that prebiotic molecules were transformed into polymers that evolved into proliferating molecular assemblages and eventually a primitive cell was first proposed about 100 years ago. To the best of our knowledge, however, no model of a proliferating prebiotic system has yet been realised because different conditions are required for polymer generation and self-assembly. In this study, we identify conditions suitable for concurrent peptide generation and self-assembly, and we show how a proliferating peptide-based droplet could be created by using synthesised amino acid thioesters as prebiotic monomers. Oligopeptides generated from the monomers spontaneously formed droplets through liquid–liquid phase separation in water. The droplets underwent a steady growth–division cycle by periodic addition of monomers through autocatalytic self-reproduction. Heterogeneous enrichment of RNA and lipids within droplets enabled RNA to protect the droplet from dissolution by lipids. These results provide experimental constructs for origins-of-life research and open up directions in the development of peptide-based materials.

Profile comparison of the 6–9 μm polycyclic aromatic hydrocarbon bands in starburst-dominated galaxies

Polycyclic aromatic hydrocarbons (PAHs) are of great astrochemical and astrobiological interest due to their potential to form prebiotic molecules. We analyse the 7.7 and 8.6 μm PAH bands in 126 predominantly starburst-dominated galaxies extracted from the Spitzer/IRS ATLAS project. Based on the peak positions of these bands, we classify them into the different A, B, and C Peeters’ classes, which allows us to address the potential characteristics of the PAH emitting population. We compare this analysis with previous work focused on the 6.2 μm PAH band for the same sample. For the first time in the literature, this statistical analysis is performed on a sample of galaxies. In our sample, the 7.7 μm complex is equally distributed in A and B object’s class while the 8.6 μm band presents more class B sources. Moreover, 39 per cent of the galaxies were distributed into A class objects for both 6.2 and 7.7 μm bands and only 18 per cent received the same A classification for the three bands. The “A A A” galaxies presented higher temperatures and less dust in their interstellar medium. Considering the redshift range covered by our sample, the distribution of the three bands into the different Peeters’ classes reveals a potential cosmological evolution in the molecular nature of the PAHs that dominate the interstellar medium in these galaxies, where B class objects seem to be more frequent at higher redshifts and, therefore, further studies have to be addressed.

Search for molecular biosignatures on Mars: laboratory simulations of UV irradiation of molecule-mineral complexes

<div> </div> <p><strong>Abstract</strong></p> <p>We present laboratory activities of preparation, characterization, and UV irradiation processing of Mars soil analogues, which are key to support both in situ exploration and sample return missions devoted to detection of molecular biosignatures on Mars.</p> <p>In detail we prepared analog mineral samples relevant to the landing sites of past, present and future Mars exploration missions, such as Gale Crater, Jezero Crater, and Oxia Planum. We doped these samples with a large variety of organic molecules (both biotic and prebiotic molecules) like amino acids, nucleotides, monosaccharides, aldehydes, lipids. We investigated molecular photostability under UV irradiation by monitoring in situ possible modifications of infrared spectroscopic features. These investigations provide pivotal information for ground analysis carried out by rovers on Mars.</p> <p><strong>Introduction</strong></p> <p>Laboratory simulations of Mars are key to support the scientific activity and technology development of life detection instruments on board present and upcoming rover missions such as Mars2020 Perseverance [1] and ExoMars2022 Rosalind Franklin [2]. Studies about the stability of organic molecules in a Martian-like environment allow us to explore the conditions for the preservation of molecular biosignatures and develop models for their degradation in the Martian geological record. A systematic study of the effects of UV radiation on a variety of molecule-mineral complexes mimicking Martian soil can be key for the selection of the most interesting samples to analyse in situ or/and collect for sample return. Testing the sensitivity of different techniques for detection of the diagnostic features of molecular biosignatures embedded into mineral matrices as a function of the molecular concentration helps the choice, design and operation of flight instruments, as well as the interpretation of data collected on the ground during mission operative periods.</p> <p><strong>Methods</strong></p> <p>Experimental analyses were conducted in the Astrobiology Laboratory at INAF-Astrophysical Observatory of Arcetri (Firenze, Italy). Laboratory activities pertain to: (i) synthesis of Mars soil analogues doped with organic compounds that are considered potential molecular biosignatures; (ii) UV-irradiation processing of the Mars soil analogues under Martian-like conditions; and (iii) spectroscopic characterization of the Mars soil analogues.</p> <p><strong>Results</strong></p> <p>Such studies have shown to be very informative in identifying mineral deposits most suitable for preservation of organic compounds, while highlighting the complementarity of different techniques for biomarkers detection, which is critical for ensuring the success of space missions devoted to the search for signs of life on Mars.</p> <p>We will present a series of laboratory results on molecular degradation caused by UV on Mars and possible application to detection of organics by Martian rovers [3,4,5,6]. In detail, we investigated the photostability of several amino acids like glycine, alanine, methionine, valine, tryptophan, phenylalanine, glutamic acid, prebiotic molecules like urea, deoxyribose and glycolaldehyde, and biomarkers like nucleotides and phytane adsorbed on relevant Martian analogs. We monitored the degradation of these molecule-mineral complexes through in situ spectroscopic analysis, investigating the reflectance properties of the samples in the NIR/MIR spectral region. Such spectroscopic characterization of molecular alteration products provides support for two upcoming robotic missions to Mars that will employ NIR spectroscopy to look for molecular biosignatures, through the instruments SuperCam on board Mars 2020, ISEM, Ma_MISS and MicrOmega on board ExoMars 2022.</p> <p><strong>Acknowledgements</strong></p> <p>This research was supported by the Italian Space Agency (ASI) grant agreement ExoMars n. 2017-48-H.0.</p> <p><strong>References</strong></p> <p>[1] Farley K. A. et al. (2020) Space Sci. Rev. 216, 142.</p> <p>[2] Vago, J. L. et al. (2017) Astrobiology 6, 309–347.</p> <p>[3] Fornaro T. et al. (2013) Icarus 226, 1068–1085.</p> <p>[4] Fornaro T. et al. (2018) Icarus 313, 38-60.</p> <p>[5] Fornaro T. et al. (2020) Front. Astron. Space Sci. 7:539289.</p> <p>[6] Poggiali G. et al. (2020) Front. Astron. Space Sci. 7:18.</p>

Charting nearby stellar systems: The intensity of Galactic cosmic rays for a sample of solar-type stars

<p>Galactic cosmic rays are important for exoplanetary atmospheres. They can contribute to the formation of hazes, prebiotic molecules and atmospheric electrical circuits. A number of so-called fingerprint ions, such as oxonium, have been identified from chemical modelling which are thought to be signatures of ionisation by energetic particles, such as Galactic cosmic rays. These fingerprint ions may be observed in exoplanetary atmospheres with upcoming JWST observations.</p> <p>I will discuss our recent results that model the propagation of Galactic cosmic rays through the stellar winds of a number of nearby solar-type stars. Our sample comprises of 5 well-observed solar-type stars that we have constructed well-constrained stellar wind models for. This allows us to calculate the transport of Galactic cosmic rays through these systems. I will present our results of the Galactic cosmic ray fluxes that reach (a) the habitable zone and (b) the location of known exoplanets. The systems show a variety of behaviour and I will discuss the most promising systems for upcoming JWST observations. </p>

The chemistry of prebiotic N-containing compounds in the atmosphere of Titan and primitive Earth beyond a holistic approach

<p> </p> <p>How did life emerge from inanimate matter? The processes that led from complex organic molecules to the first self-replicating systems are no longer at play and we cannot easily reconstruct them because we do not have a geological record of the period when the transition from simple molecules to the very first forms of “life” have occurred. The presence of stable hydrosphere is considered as the first milestone in the timeline of the abiotic origin of life theory, with the second milestone being the massive accumulation of organic compounds necessary for the transition from organic chemistry to the biochemistry of life. But how Earth became so rich in complex organic molecules – up to the point that life spontaneously evolved from them - is still a matter of debate. At that stage, the abundance of liquid water, indeed, represents an obstacle for organic synthesis. Two theories have been suggested to solve this paradox, which are usually referred to as <em>endogenous synthesis</em> and <em>exogenous synthesis</em> scenarios [1]. But in both cases, prebiotic molecules (that is, molecules which are simple to be formed in abiotic processes but contain the functional groups typical of biological molecules or have the capability to easily evolve into them) are formed in gaseous media. Indeed, gas-phase prebiotic molecules have been observed in the upper atmosphere of Titan, the massive moon of Saturn, as well as in the interstellar clouds and cometary comae.</p> <p>The comprehension of the chemical processes that lead from simple atomic/diatomic species to prebiotic complex chemicals is an important part of the study on the origin of life. The study of these preliminary steps might seem relatively simple compared to the characterization of the other unknown phenomena that have led to the first living organisms. Nevertheless, the formation mechanisms of many of the prebiotic molecules that we observe nowadays in proto-stellar clouds or comets/meteorites or planetary atmospheres are far from being understood, while a comprehension of those processes can certainly help to set the stage for the emergence of life to occur.</p> <p>For this reason, in our laboratory we have started a systematic investigation of gas-phase reactions leading to simple prebiotic molecules within the Italian National Project of Astrobiology—Life in Space—Origin, Presence, Persistence of Life in Space, from Molecules to Extremophiles [2].</p> <p>In particular, by combining an experimental and theoretical approach, we have investigated a series of bimolecular reactions under single collision conditions. The aim is to provide detailed information on the elementary reactions which are employed in photochemical models of planetary atmosphere and cometary comae [3]. In particular, we have investigated several reactive systems leading to the formation of nitriles (such as dicyanoacetylene) and imines (such as ethanimine), as well as reactive radicals that can further react in subsequent reactions. We have also investigated reactions involving nitrogen atoms and aromatic compounds (benzene, pyridine, toluene) to address the role of these compounds in the growth of N-containing aromatic compounds, a proxy of DNA and RNA bases. In this contribution, the main results concerning the reactions involving atomic nitrogen, N, or cyano radicals, CN, and cyanoacetylene, acrylonitrile, benzene, toluene and pyridine will be illustrated and the implications for prebiotic chemistry noted.</p> <p>[1] C. Chyba and C. Sagan. Nature 1992, 355, 125.</p> <p>[2] S. Onofri, N. Balucani, V. Barone et al. Astrobiology 2020, 20, 580. DOI: 10.1089/ast.2020.2247</p> <p>[3] N. Balucani. Physics of Life Reviews 2020, 34–35, 136. DOI: 10.1016/j.plrev.2019.03.0061571-0645</p>

The intensity of energetic particles at the evolving Earth

<p>Energetic particles can drive the formation of prebiotic molecules in exoplanetary which are important for the origin of life. On the other hand, large energetic particle fluxes are known to be detrimental to developed life by damaging DNA. Thus, in order to understand the origin, and subsequent survival, of life on Earth it is necessary to first understand the energetic particle fluxes incident on Earth at that time. There are two types of energetic particles that are important: stellar energetic particles accelerated by their host star and Galactic cosmic rays.</p> <p>I will present our recent results that model the propagation of these energetic particles through the wind of a Sun-like star during its lifetime. We find, at the time when life is thought to have begun on Earth, that Galactic cosmic ray fluxes were greatly suppressed in comparison to present-day values. However, I will show that stellar energetic particle fluxes would have been larger than present-day values. I motivate that the maximum stellar energetic particle energy increases for younger stars. This is extremely important because higher energy particles are more likely to impact the surface of a planet, in addition to its atmosphere. I will briefly discuss how we applied our model to an exoplanetary system and how this can be linked to upcoming observations.</p>