Hyman Hartman

Low temperature hydrothermal maturation of organic matter in sediments from the Atlantis II Deep, Red Sea

Hydrocarbons and bulk organic matter of two sediment cores (No. 84 and 126, CHAIN 61 cruise) located within the Atlantis II Deep have been analyzed. Although the brines overlying the coring areas were reported to be sterile, microbial inputs and minor terrestrial sources the major sedimentary organic material. This input is derived from the upper water column above the brines. Both steroid and triterpenoid hydrocarbons show that extensive acid-catalyzed reactions are occurring in the sediments. In comparison with other hydrothermal (Guaymas Basin) or intrusive systems (Cape Verde Rise), the Atlantis II Deep exhibits a lower degree of thermal maturation. This is easily deduced from the elemental composition of the kerogens and the absence of polynuclear aromatic hydrocarbons of a pyrolytic origin in the bitumen. The lack of carbon number preference among the n-alkanes suggests, especially in the case of the long chain homologs, that the organic matter of Atlantis II Deep sediments has undergone some degree of catagenesis. However, the yields of hydrocarbons are much lower than those observed in other hydrothermal areas. The effect of lower temperature and poor source-rock characteristics appear to be responsible for the differences.

Enceladus: Cassini observations and implications for the search for life

Aims. The recent Cassini discovery of water vapor plumes ejected from the south pole of the Saturnian satellite, Enceladus, presents a unique window of opportunity for the detection of extant life in our solar system. Methods. With its significant geothermal energy source propelling these plumes >80 km from the surface of the moon and the ensuing large temperature gradient with the surrounding environment, it is possible to have the weathering of rocks by liquid water at the rock/liquid interface. For the cases of the putatively detected salt-water oceans beneath the ice crusts of Europa and Callisto, an isolated subsurface ocean without photosynthesis or contact with an oxidizing atmosphere will approach chemical equilibrium and annihilate any ecosystems dependent on redox gradients unless there is a substantial alternative energy source. This thermodynamic tendency imposes severe constraints on any biota that is based on chemical energy. On Enceladus, the weathering of rocks by liquid water and any concomitant radioactive emissions are possible incipient conditions for life. If there is CO, CO2 and NH3 present in the spectra obtained from the plume, then this is possible evidence that amino acids could be formed at the rock/liquid interface of Enceladus. The combination of a hydrological cycle, chemical redox gradient and geochemical cycle give favorable conditions for life. Results. We discuss the search for signatures of these species and organics in the Cassini UVIS spectra of the plume and implications for the possible detection of life.

The Evolution of the Ribosome and the Genetic Code

The evolution of the genetic code is mapped out starting with the aminoacyl tRNA-synthetases and their interaction with the operational code in the tRNA acceptor arm. Combining this operational code with a metric based on the biosynthesis of amino acids from the Citric acid, we come to the conclusion that the earliest genetic code was a Guanine Cytosine (GC) code. This has implications for the likely earliest positively charged amino acids. The progression from this pure GC code to the extant one is traced out in the evolution of the Large Ribosomal Subunit, LSU, and its proteins; in particular those associated with the Peptidyl Transfer Center (PTC) and the nascent peptide exit tunnel. This progression has implications for the earliest encoded peptides and their evolutionary progression into full complex proteins.

What Does the Microsporidian E. cuniculi Tell Us About the Origin of the Eukaryotic Cell

The relationship among the three cellular domains Archaea, Bacteria, and Eukarya has become a central problem in unraveling the tree of life. This relationship can now be studied as the completely sequenced genomes of representatives of these cellular domains become available. We performed a bioinformatic investigation of the Encephalitozoon cuniculi proteome. E. cuniculi has the smallest sequenced eukaryotic genome, 2.9 megabases coding for 1997 proteins. The proteins of E. cuniculi were compared with a previously characterized set of eukaryotic signature proteins (ESPs). ESPs are found in a eukaryotic cell, whether from an animal, a plant, a fungus, or a protozoan, but are not found in the Archaea and the Bacteria. We demonstrated that 85% of the ESPs have significant sequence similarity to proteins in E. cuniculi. Hence, E. cuniculi, a minimal eukaryotic cell that has removed all inessential proteins, still preserves most of the ESPs that make it a member of the Eukarya. The locations and functions of these ESPs point to the earliest history of eukaryotes.

The evolution of Class II Aminoacyl-tRNA synthetases and the first code.

Class II Aminoacyl‐tRNA synthetases are a set of very ancient multi domain proteins. The evolution of the catalytic domain of Class II synthetases can be reconstructed from three peptidyl‐hairpins. Further evolution from this primordial catalytic core leads to a split of the Class II synthetases into two divisions potentially associated with the operational code. The earliest form of this code likely coded predominantly Glycine (Gly), Proline (Pro), Alanine (Ala) and “Lysine”/Aspartic acid (Lys/Asp). There is a paradox in these synthetases beginning with a hairpin structure before the Genetic Code existed. A resolution is found in the suggestion that the primordial Aminoacyl synthetases formed in a transition from a Thioester world to a Phosphate ester world.

The evolution of the cilium and the eukaryotic cell

The Cilium, the Nucleus and the Mitochondrion are three important organelles whose evolutionary histories are intimately related to the evolution and origin of the eukaryotic cell. The cilium is involved in motility and sensory transduction. The cilium is only found in the eukaryotic cells. Here we show that eight gene duplications prior to the last common ancestor of all extant eukaryotes account for the expansion of the Heavy Chain Dynein family of motor proteins and the evolution of the complexity of the cilium. The ambiguities in the branching of the phylogenetic tree of the HC-Dyneins were resolved by creating well-defined subtrees and using them to create the full tree. Due to the intimate relationship between the nucleus, the division center, mitosis and the basal body/centriole, the evolution of the cilium can now be related to the evolution of mitosis. In addition, the analysis of the cilium rules out its endosymbiotic origin from a phagocytosis of a bacterium.

Formation of Replicating Saponite from a Gel in the Presence of Oxalate: Implications for the Formation of Clay Minerals in Carbonaceous Chondrites and the Origin of Life

The potential role of clay minerals in the abiotic origin of life has been the subject of ongoing debate for the past several decades. At issue are the clay minerals found in a class of meteorites known as carbonaceous chondrites. These clay minerals are the product of aqueous alteration of anhydrous mineral phases, such as olivine and orthopyroxene, that are often present in the chondrules. Moreover, there is a strong correlation in the occurrence of clay minerals and the presence of polar organic molecules. It has been shown in laboratory experiments at low temperature and ambient pressure that polar organic molecules, such as the oxalate found in meteorites, can catalyze the crystallization of clay minerals. In this study, we show that oxalate is a robust catalyst in the crystallization of saponite, an Al- and Mg-rich, trioctahedral 2:1 layer silicate, from a silicate gel at 60°C and ambient pressure. High-resolution transmission electron microscopy analysis of the saponite treated with octadecylammonium (n(C)=18) cations revealed the presence of 2:1 layer structures that have variable interlayer charge. The crystallization of these differently charged 2:1 layer silicates most likely occurred independently. The fact that 2:1 layer silicates with variable charge formed in the same gel has implications for our understanding of the origin of life, as these 2:1 clay minerals most likely replicate by a mechanism of template-catalyzed polymerization and transmit the charge distribution from layer to layer. If polar organic molecules like oxalate can catalyze the formation of clay-mineral crystals, which in turn promote clay microenvironments and provide abundant adsorption sites for other organic molecules present in solution, the interaction among these adsorbed molecules could lead to the polymerization of more complex organic molecules like RNA from nucleotides on early Earth.

THE INFLUENCE OF OXALATE-PROMOTED GROWTH OF SAPONITE AND TALC CRYSTALS ON RECTORITE: TESTING THE INTERCALATION-SYNTHESIS HYPOTHESIS OF 2:1 LAYER SILICATES

The intercalating growth of new silicate layers or metal hydroxide layers in the interlayer space of other clay minerals is known from various mixed-layer clay minerals such as illite-smectite (I-S), chlorite-vermiculite, and mica-vermiculite. In a recent study, the present authors proposed that smectitegroup minerals can be synthesized from solution as new 2:1 silicate layers within the low-charge interlayers of rectorite. That study showed how oxalate catalyzes the crystallization of saponite from a silicate gel at low temperatures (60ºC) and ambient pressure. As an extension of this work the aim of the present study was to test the claim that new 2:1 silicate layers can be synthesized as new intercalating layers in the low-charge interlayers of rectorite and whether oxalate could promote such an intercalation synthesis. Two experiments were conducted at 60ºC and atmospheric pressure. First, disodium oxalate solution was added to a suspension of rectorite in order to investigate the effects that oxalate anions have on the structure of rectorite. In a second experiment, silicate gel of saponitic composition (calculated interlayer charge -0.33 eq/O10(OH)2) was mixed with a suspension of rectorite and incubated in disodium oxalate solution. The synthesis products were extracted after 3 months and analyzed by X-ray diffraction and high-resolution transmission electron microscopy (HRTEM). The treatment of ultrathin sections with octadecylammonium (nC =18) cations revealed the presence of 2:1 layer silicates with different interlayer charges that grew from the silicate gel. The oxalate-promoted nucleation of saponite and talc crystallites on the rectorite led to the alteration and ultimately to the destruction of the rectorite structure. The change was documented in HRTEM lattice-fringe images. The crystallization of new 2:1 layer silicates also occurred within the expandable interlayers of rectorite but not as new 2:1 silicate layers parallel to the previous 2:1 silicate layers. Instead, they grew independently of any orientation predetermined by the rectorite crystal substrate and their crystallization was responsible for the destruction of the rectorite structure.

Phage in the time of cholera.

A team at Tufts Medical School recently reported [1], in Nature Communications, that using viruses (phages) that infect the bacteria may be able to do just that. They found that giving animals (mice and rabbits) a cocktail of three phages that infect V. cholerae, before infecting with live bacteria, resulted in protection of the mice from the bacterial infection. When these viruses, or phages, infect a bacterial cell and replicate, they kill the bacterial cell in the process.

Erratum: Catalyzed Synthesis of Zinc Clays by Prebiotic Central Metabolites

A correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper.